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 IEDB IEDB http://www.partec.de/products/cyflow.html John Quinn A CyFlow_Sl is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels. CyFlow SL CyFlow SL Haemophilus influenzae Haemophilus influenzae Streptococcaceae Streptococcaceae The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) JY cell culture IEDB IEDB JY cell culture Awaiting English definition from Monnie McGee spread calculation objective spread calculation objective James Malone OBI: workshop A material entity that has the material sample role material sample material sample blood drawn from patient to measure his systemic glucose level. Daniel Schober Melanie Courtot Frank Gibson Bill Bug A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material. freeze function freeze function CHEF gel box, slab gel box, capillary electrophoresis Frank Gibson electrophoresis box electrophoresis unit Kevin Clancy sep:00095 gel tank gel tank A gel tank is a device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules. Xylella fastidiosa Xylella fastidiosa An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008 OBI, CDISC role of Institutional Review Board Jennifer Fostel role of Institutional Review Board Urochordata Urochordata DNA cleavage, restriction analysis restriction enzyme assay DNA cleavage, restriction analysis the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components PERSON:Kevin Clancy the use of enzymes to cut DNA molecules, the study of DNA through cleavage, mapping, and analysis of the fragments Filicophyta Filicophyta IEDB a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme Bjoern Peters changed from synthetic polypeptide to peptide, to get rid of the restriction of having more than 10 amino acids (required by Chebi). synthetic peptide mixed argon-krypton gas laser mixed argon-krypton gas laser argon-krypton laser in a cytometer A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer. John Quinn http://www.eio.com/repairfaq/sam/laserarg.htm blood plasma is a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. PERSON: Philippe Rocca-Serra PERSON: Maura Gasparetto blood plasma blood plasma PERSON: Melanie Courtot PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings. This is in FMA WEB: http://en.wikipedia.org/wiki/Blood_plasma plasma Collembola Collembola gas filter function gas filter function A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture Frank Gibson Hominidae Hominidae Bacteroidetes/Chlorobi group Bacteroidetes/Chlorobi group PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086 atomic emission detector Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element. WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt> AED atomic emission detector PERSON: Luisa Montecchi GROUP: PSI Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications. PMID:6110205. collection of cDNA derived from mouse splenocytes. PERSON: Philippe Rocca-Serra cDNA library cDNA library Rubrobacter xylanophilus Rubrobacter xylanophilus WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php> PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238 A Varian NMR spectrometer. Varian VXR spectrometer Varian VXR spectrometer Viannia Viannia should be imported from chebi nucleic acid nucleic acid Frank Gibson http://en.wikipedia.org/wiki/Chromatography chromatography instrument A Chromatography device is a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. chromatography device chromatography device Antirrhinum majus Antirrhinum majus The process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule. MHC:epitope complex binding to TCR IEDB MHC:epitope complex binding to TCR IEDB regression analysis method Tina Hernandez-Boussard BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048 Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data. regression analysis method Drosophila orena Drosophila orena Dechloromonas Dechloromonas Ryan Brinkman peak matching peak matching Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold PERSON: Ryan Brinkman James Malone A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously multiple comparison correction objective http://en.wikipedia.org/wiki/Multiple_Testing_Correction Application of the Bonferroni correction multiple testing correction objective multiple testing correction objective http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105 GROUP:<http://msi-ontology.sourceforge.net> An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. ion exchange column ion exchange column PERSON:Daniel Schober Aconoidasida Aconoidasida Lactococcus Lactococcus Brucella abortus Brucella abortus standard deviation calculation standard deviation calculation Monnie McGee A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean. PERSON: Monnie McGee subgraph degree calculation PERSON: Richard Scheuermann Richard Scheuermann A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph. subgraph degree calculation Digenea Digenea Pseudomonadales Pseudomonadales Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. DS: Probably better modeled as a role. bead bead A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules. OBI GROUP: Role branch Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia. A nutrient role is a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment. Wikipedia, feb 29, 2008 nutrient role nutrient role A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector. recombinant vector recombinant vector column cartridge column cartridge http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober T cell epitope intracellular cytokine staining (ICS) IFN-g assay T cell epitope intracellular cytokine staining (ICS) IFN-g assay A T cell epitope specific cytokine production assay that measures production of IFN-g by T cells utilizing the ICS methodology. IEDB IEDB Trypanosoma brucei Trypanosoma brucei temperature control bath Frank Gibson temperature control bath OBI Instrument branch Alan Ruttenburg VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. Daniel Schober A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. Desulfovibrionaceae Desulfovibrionaceae Chlorophyceae Chlorophyceae Apoidea Apoidea Sinorhizobium/Ensifer group Sinorhizobium/Ensifer group Sordariaceae Sordariaceae Bilateria Bilateria http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231 PERSON:Daniel Schober An NMR probe that is manufactured by Bruker. Bruker NMR probe Bruker NMR probe GROUP:<http://msi-ontology.sourceforge.net> chromatin immunoprecipitation sequencing assay ChIP-SEQ assay adapted from Wikipedia PMID: 19275939 ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9. Philippe Rocca-Serra is an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. ChIP-SEQ assay interleukin-21 production interleukin-21 production The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Noctuidae Noctuidae Mycetozoa Mycetozoa Rhodocyclaceae Rhodocyclaceae Streptosporangineae Streptosporangineae James Malone dye swap merge PERSON: James Malone PERSON: Elisabetta Manduchi Elisabetta Manduchi A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met. dye swap merge Bartonella henselae Bartonella henselae blood coagulation blood coagulation The sequential process by which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers. is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. glucose tolerance test Philippe Rocca-Serra PMID: 19527607 Using the 100-g Oral Glucose Tolerance Test to Predict Fetal and Maternal Outcomes in Women with Gestational Diabetes Mellitus. Lin CH, Wen SF, Wu YH, Huang MJ. Chang Gung Med J. 2009 May-Jun;32(3):283-9. NuGO OBI plan branch glucose tolerance test Moss Superclass V Moss Superclass V Onchocercidae Onchocercidae interleukin-15 production interleukin-15 production The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Joseph Spliden Elisabetta Manduchi biexponential transformation biexponential transformation Ryan Brinkman A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation. This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf commelinids commelinids Staphylococcus aureus subsp. aureus Staphylococcus aureus subsp. aureus is the transplantation of living cells, tissues or organs from one species to another such as from pigs to humans xenotransplantation OBI branch derived xenotransplantation PlanAndPlannedProcess Branch A dose of medicine or placebo in the form of a small pellet. Person:Alan Ruttenberg pill pill http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel proxy respondent role proxy respondent role Jennifer Fostel Acanthomorpha Acanthomorpha tecmag EAGLE probe tecmag EAGLE probe The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248 GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober Glass Array Hybridization Cassette A container which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide. hybridization chamber hybridization chamber Trish Whetzel MO Jennifer Fostel principal investigator role principal investigator role Principal investigator is a responsible party role played by a person responsible for the overall conduct of a study Methanosarcina mazei Methanosarcina mazei Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group eligibility rule an eligibility rule (criterion) is_a *rule* which defines the positive and negative criteria decide an entity to enter a study and that will define the population of the study PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3. eligibility rule PRS is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length. true single molecule sequencing Philippe Rocca-Serra Helicos sequencing PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9. adapted from wikipedia Helicos sequencing http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199 Bruker Metabolic Profiler PERSON:Daniel Schober An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis. Bruker Metabolic Profiler WEB:<http://www.bruker-biospin.com/metabolicprofiler.html> Rhizobiaceae Rhizobiaceae renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms IEDB is process in which a material substance is added to a cell culture adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient adding substance to cell culture Bjoern Peters adding substance to cell culture DNA extraction DNA extraction OBI branch derived PlanAndPlannedProcess Branch A DNA extraction is a nucleic acid extraction where the desired output material is DNA. James Malone A partitioning data transformation is a data transformation that has objective partitioning. partitioning data transformation partitioning data transformation PERSON: James Malone GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober gas chromatography equipment gas chromatography equipment http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030 Any device used in a gas chromatography experiment. Rickettsia conorii Rickettsia conorii A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. CD8 This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. WEB: http://en.wikipedia.org/wiki/CD8 CD8 receptor CD8 receptor Measurment of the radioactivity of a supernatant, as in chromium_release_assay. An assay in which a material's radioactivity is measured. radioactivity detection OBI branch derived PlanAndPlannedProcess Branch radioactivity detection Malacostraca Malacostraca polystyrene tube polystyrene tube PERSON: Chris Stoeckert a polystyrene tube is a test tube made of polystyrene PERSON: Chris Stoeckert Polystyrene tubes can be used to contain tissue culture cells during centrifgation Azotobacter vinelandii Azotobacter vinelandii IEDB A cell culture including cells that have an effector T cell function culture of effector T cells culture of effector T cells A culture of cytotoxic CD8+ T cells. Elisabetta Manduchi Melanie Courtot ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 James Malone Ryan Brinkman logistic-log curve fitting A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n). logistic-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 a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve. GROUP:<http://msi-ontology.sourceforge.net> Bruker MATCH tube holder system PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211 The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications. The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. Bruker MATCH tube holder system Bruker Multiple Adjustable Tube Clamp Holder Halobacterium sp. Halobacterium sp. charge plate John Quinn LSR2 charge plate charge plate Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting. a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument microscope slide PERSON: Phillippe Rocca-Serra OBI biomaterial branch PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay. microscope slide http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192 high resolution magic angle spin probe high resolution magic angle spin probe high resolution MAS, hr-MAS PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. defprov: Bruker website alt High resolution MAS (hr-MAS) provides an easy means of obtaining high resolution spectra for a variety of samples that would otherwise result in poorly resolved spectra. The addition of an hr-MAS probe and a MAS pneumatic unit to a standard high resolution spectrometer is all that is needed to open the gate to the world of hr-MAS spectroscopy and gain access to a vast amount of highly interesting samples. Mammalia Mammalia is an assay where the output data is a datum with one of two values denoted success and failure. OBI branch derived Bernoulli trial Bernoulli trial PlanAndPlannedProcess Branch Melanie Courtot magnify function Daniel Schober Bill Bug magnify function A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path. Frank Gibson Equus caballus Equus caballus Actinobacillus Actinobacillus Thermoplasma volcanium Thermoplasma volcanium Mandibulata Mandibulata WEB: http://en.wikipedia.org/wiki/Exponential_function Elisabetta Manduchi exponential transformation exponential transformation An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function. WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function Nematoda Nematoda A molecular crosslinker is an instrument that is able to chemically join two or more molecules. MO MO molecular crosslinker Trish Whetzel molecular crosslinker molecular crosslinker Stratalinker AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly. Tremellomycetidae Tremellomycetidae Alteromonadaceae Alteromonadaceae Magnaporthaceae Magnaporthaceae fractional factorial design A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run Philippe Rocca-Serra http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control fractional factorial design Cellia Cellia Leishmania mexicana species complex Leishmania mexicana species complex Sus scrofa Sus scrofa Percomorpha Percomorpha Magnetospirillum Magnetospirillum Fusobacteriaceae Fusobacteriaceae Ferroplasmaceae Ferroplasmaceae Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material recombinant BAC cloning http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome recombinant BAC cloning data vector reduction objective data vector reduction objective PERSON: Richard H. Scheuermann Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k. James Malone Richard H. Scheuermann class discovery objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. PERSON: James Malone discriminant analysis objective clustering objective class discovery objective unsupervised classification objective PERSON: Elisabetta Manduchi James Malone PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell cell capsule shell http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n capsule shell Person:Alan Ruttenberg a small rounded gelatinous container Synechococcus Synechococcus Lolium Lolium Arabidopsis Arabidopsis organ harvesting organ harvesting IEDB IEDB The process of removing an organ from its source organism quartz cuvette flow chamber quartz cuvette flow chamber CVF-Q-10 flow chamber, CV-Q-10 flow chamber A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells. http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm John Quinn OBI and Li-Cor is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing Li-Cor 4300 DNA Analysis System Li-Cor 4300 DNA Analysis System Philippe Rocca-Serra Philippe Rocca-Serra Li-Cor Li-Cor the manufacturer role of Li-Cor the manufacturer role of Li-Cor 0.01, 0.03 A parameter threshold is a datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role parameter threshold parameter threshold person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt Mycobacterium leprae Mycobacterium leprae Ustilago maydis Ustilago maydis MA transformation Elisabetta Manduchi MA transformation PERSON: Elisabetta Manduchi MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2. An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation. Philippe Rocca-Serra hardware testing objective hardware testing objective Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner. Jennifer Fostel Cluster of the lymphocytes population. person:Allyson cluster person:Chris Stoeckert group:OBI A data cluster is a data set which is a subset of data that are a similar to each other in some way. cluster Jennifer Fostel baseline participant role baseline participant role is a reference participant role which is realized by making the reference to qualities at the start of the study or intervention baseline participant role Subject at time = 0; subject before a stress test. epitope specific killing by T cells epitope specific killing by T cells A biological process where T cells lyse antigen presenting cells resulting from the recognition of a T cell epitope on MHC molecules of the antigen presenting cell. IEDB IEDB Actinomycetaceae Actinomycetaceae Philippe Rocca-Serra single fragment library single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs fragment library randomized complete block design Philippe Rocca-Serra http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd)) http://www.tufts.edu/~gdallal/ranblock.htm A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups. randomized complete block design PPPB branch is the specification of an objective to determine a specified type of information about an evaluated entity (independent continuant bearing evaluant role) assay objective assay objective PPPB branch the objective to determine the weight of a mouse. 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. PERSON: Chris Stoeckert independent variable specification independent variable specification PERSON: Bjoern Peters PERSON: Alan Ruttenberg Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled Deuterostomia Deuterostomia denatured polymer denatured polymer PERSON: Alan Ruttenberg Is a polymer which has lost secondary or tertiary structure http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 Coniferopsida Coniferopsida OBI-Branch Philippe Rocca-Serra storage PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10. storage is a process by which material entities are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability storage Rickettsia sibirica Rickettsia sibirica chemokine production chemokine production The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. A physical quality inhering in an entity exhibiting the physical characteristics of a solid. A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. quality of a solid quality of a solid Crocosphaera Crocosphaera The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. high resolution probe with automatic tuning and matching http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224 High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM high resolution probe with automatic tuning and matching GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober Carnivora Carnivora person:Jennifer Fostel CDISC glossary An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators. electronic case report tabulation electronic case report tabulation Leymus Leymus IEDB IEDB epitope specific IL-10 release by T cells epitope specific IL-10 release by T cells A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope. the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial enzymatic DNA replication enzymatic DNA replication OBI branch derived PERSON:Kevin Clancy the use of enzymes to duplicate DNA molecules Phasianidae Phasianidae Saccharomyces paradoxus Saccharomyces paradoxus Trish Whetzel DNA sequencer DNA sequencer A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences. ABI 377 DNA Sequencer, ABI 310 DNA Sequencer MO Pasteuria nishizawae Pasteuria nishizawae IEDB IEDB antigen antigen is a material entity that has the antigen role polymerization PRS:22102008: need to import catalyst from CHEBI 35223 Philippe Rocca-Serra polymerization PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3. OBI-Branch polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight Populus euphratica Populus euphratica Amphiesmenoptera Amphiesmenoptera IEDB IEDB epitope specific IL-13 release by T cells epitope specific IL-13 release by T cells A biological process where T cells produce IL-13 resulting from the recognition of a T cell epitope. Euglenozoa Euglenozoa Coniferophyta Coniferophyta Bruker LC-NMR/MS platform Bruker LC-NMR/MS platform GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277 Includes the connection to a high-resolution TOF-LC-MS system. Acidithiobacillus Acidithiobacillus IEDB epitope specific IL-18 release by T cells epitope specific IL-18 release by T cells IEDB A biological process where T cells produce IL-18 resulting from the recognition of a T cell epitope. Anophelinae Anophelinae Schizotrypanum Schizotrypanum flow cell Biofilm Flow Cell John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. flow cell placeholder for SO a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. BP et al primary structure of DNA macromolecule primary structure of DNA macromolecule Ustilaginomycetes Ustilaginomycetes Enterobacteriales Enterobacteriales Pooideae Pooideae Geobacteraceae Geobacteraceae cloning vector cloning vector A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site. Funariales Funariales Amniota Amniota unclassified Burkholderiales unclassified Burkholderiales Desulfovibrio Desulfovibrio Leishmania donovani Leishmania donovani A clustered data set is a data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. A clustered data set is the output of a K means clustering data transformation clustered data set PERSON: Monnie McGee PERSON: James Malone data set with assigned discovered class labels clustered data set The fluorescent reporter intensity is a datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. fluorescent reporter intensity group:OBI person:Chris Stoeckert fluorescent reporter intensity Desulfuromonadales Desulfuromonadales An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized. WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> Bruker Ultrastabilized NMR magnet Bruker Ultrastabilized NMR magnet http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188 PERSON:Daniel Schober Ascomycota Ascomycota Bacillaceae Bacillaceae Frank Gibson A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture liquid filter function liquid filter function statistical model validation http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia Leishmania [NCBITaxon:38568] Leishmania [NCBITaxon:38568] Naturally occurring polyribonucleotides. ribonucleic acids ribonucleic acids Acoelomata Acoelomata Moorella group Moorella group tumor necrosis factor production tumor necrosis factor production The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Paxilineae Paxilineae A false discovery rate correction method is a multiple testing procedure that controls for the expected value of the proportion of false positives among the rejected hypotheses. Monnie McGee FDR correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 false discovery rate correction method false discovery rate correction method concentrate Evaporation of the solution containing DNA to increase the concentration of the DNA molecules PERSON:Kevin Clancy a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material concentrate OBI branch derived Fabales Fabales A cytometer is an instrument for counting and measuring cells. cytometer cytometer Melanie Courtot http://medical.merriam-webster.com/medical/cytometer A relational spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. right side of right side of A relational spatial quality where on entity is located on right side of a another entity. PERSON: Tina Boussard spectrum analysis objective spectrum analysis objective http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090 PERSON:Daniel Schober The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis. PID photoionization detector photoionization detector WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm> The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. manual injection system manual injection system http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064 GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober Chlamydomonadaceae Chlamydomonadaceae Paracoccidioides Paracoccidioides Drosophila sechellia Drosophila sechellia Philippe Rocca-Serra OBI Instrument adapted from Wikipedia syringe Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832 a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw syringe Alphaproteobacteria Alphaproteobacteria group assignment Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation group assignment group assignment is a process which has an organism as specified input and during which a role is assigned OBI Plan cohort assignment study assignment Philippe Rocca-Serra James Malone Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type. gene list visualization gene list visualization PERSON: Melanie Courtot A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. PERSON: Maura Gasparetto blood serum specimen WEB: http://en.wikipedia.org/wiki/Blood_plasma PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy. PERSON: Philippe Rocca-Serra blood serum specimen http://www.cytobuoy.com/ A CytoBuoy is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. John Quinn, Melanie Courtot CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations CytoBuoy CytoBuoy Melanie Courtot loess group transformation loess group transformation Elisabetta Manduchi A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs. OTHER: Editor's generalization based on MGED Ontology term James Malone Philippe Rocca-Serra Orbiliales Orbiliales sine transformation sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc. sine transformation A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html. WEB: http://mathworld.wolfram.com/Sine.html Elisabetta Manduchi Populus Populus animal feeding branch derived In an investigation, this will typically be part of an animal care process Bjoern Peters animal feeding giving crickets to a snake. animal feeding is a process in which animals are provided with food data set of features data set of features PERSON: Monnie McGee PERSON: James Malone A data set of features is a data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set. nucleotide overhang cloning nucleotide overhang cloning Helen Parkinson Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation Treponema pallidum Treponema pallidum Coregonus clupeaformis Coregonus clupeaformis Silurana Silurana PMID:16762068 Philippe Rocca-Serra Elisabetta Manduchi autoscaling unit-variance scaling A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable. unit-variance scaling Salmonella Salmonella JEOL CapNMR probe JEOL CapNMR probe WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx> PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233 The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 µl flowcell with an NMR active volume of 2.5 µl, and a 10 µl flowcell with an NMR active volume of 5 µl. The fluidic connections are 75 µm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility. Mesoplasma florum Mesoplasma florum Xanthomonas campestris pv. campestris Xanthomonas campestris pv. campestris Anaplasmataceae Anaplasmataceae soft independent modeling of class analogy analysis Tina Hernandez-Boussard Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes. SIMCA WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies soft independent modeling of class analogy analysis Candida glabrata Candida glabrata syringe pump John Quinn NE-1000 Single Syringe Pump http://www.answers.com/topic/syringe, 2007-05-11 syringe pump Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates. Apis Apis Buchnera sp. Buchnera sp. averaging objective Elisabetta Manduchi A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment. PERSON: Elisabetta Manduchi averaging objective James Malone An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. Crocosphaera watsonii Crocosphaera watsonii Mycosphaerella Mycosphaerella T cell epitope ELISPOT IL-4 assay IEDB T cell epitope ELISPOT IL-4 assay IEDB A T cell epitope specific cytokine production assay that measures production of IL-4 by T cells utilizing the ELISPOT methodology. Archaeoglobus Archaeoglobus the manufacturer role of Helicos the manufacturer role of Helicos Philippe Rocca-Serra Helicos Helicos Philippe Rocca-Serra http://www.helicosbio.com/Products/HelicostradeGeneticAnalysisSystem/HeliScopetradeSequencer/tabid/87/Default.aspx HeliScope Single Molecule Sequencer HeliScope Single Molecule Sequencer is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry Rhodobacterales Rhodobacterales A data set of predicted values according to fitted curvet is a data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. data set of predicted values according to fitted curve data set of predicted values according to fitted curve PERSON: Monnie McGee PERSON: James Malone A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. OBI Instrument branch OBI Instrument branch microarray platform microarray platform An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens antigen role OBI antigen role Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response Role Branch CD8-positive, alpha-beta cytotoxic T cell CD8-positive, alpha-beta cytotoxic T cell A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. Nectriaceae Nectriaceae PERSON: Richard Scheuermann A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph. Richard Scheuermann weighted network graph construction weighted network graph construction Pleuronectidae Pleuronectidae IEDB allergy IEDB is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect allergy Halobacterium Halobacterium Philippe Rocca-Serra OBI plan and planned process branch is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity immunoprecipitation PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. immunoprecipitation interleukin-3 production interleukin-3 production The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Coxiellaceae Coxiellaceae Lepidium sativum Lepidium sativum Rubrobacteridae Rubrobacteridae Cannabis Cannabis Nicotiana benthamiana Nicotiana benthamiana Bacteroidetes Bacteroidetes Streptococcus suis Streptococcus suis Mutisioideae Mutisioideae Philippe Rocca-Serra PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed. 2x2 factorial design PMID: 17561240 2x2 factorial design 2x2 factorial design is factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors Synechococcus elongatus Synechococcus elongatus fragment derived from protein A material entity which is derived from a protein fragment derived from protein GROUP: IEDB PERSON: Bjoern Peters original term: protein fragment split into synthetic polypeptide and fragment derived from protein THE DEFINITION OF THIS SUGGESTS WE COVER THIS ALREADY IN PEPTIDE/POLYPETIDE. DO WE NEED THIS AND CAN WE DEAL WITH IT IN SOME OTHER WAY? JAMES the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme PRS:22022008. result from protocol_application where input=protein and output=polypeptide or peptide (to capture: derives_from protein) edited information edited information Philippe Rocca-Serra Pasteurellaceae Pasteurellaceae Philippe Rocca-Serra is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers. ABI 377 automated sequencer ABI 377 automated sequencer Applied Biosystems Rattus norvegicus Rattus norvegicus image cytometer http://web.mit.edu/solab/Research/ImageCytometry.html Melanie Courtot image cytometer An image_cytometer is an instrument for image-based study or measurement of cells. The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining. Chlamydophila pneumoniae Chlamydophila pneumoniae PERSON: Daniel Schober Daniel Schober water bath water bath A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). heart heart MC: should be imported Burkholderia Burkholderia Frank Gibson Melanie Courtot A syringe, a beaker Bill Bug A contain function is a function to bound or constrain some quantity of material in some space contain function contain function Daniel Schober Ascidiacea Ascidiacea A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope. PERSON: Helen Parkinson Helen Parkinson b cell epitope prediction b cell epitope prediction polymerase chain reaction adapted from wikipedai PCR Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 OBI Plan polymerase chain reaction PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified. Neognathi Neognathi Mouth Mouth oral ingestion of pill oral ingestion of pill Person:Alan Ruttenberg An adding a material entity to target with the entity is a pill and the target is the mouth Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. membrane-bounded organelle membrane-bounded organelle Aves Aves Liriodendron Liriodendron The presentation of a flashing light to a monkey during reward training presentation of stimulus Helen Parkinson, Jessica Turner, Dirk Derom presentation of stimulus Helen Parkinson, Jessica Turner, Dirk Derom a planned process in which an organism is exposed to some stimulus with the intent to invoke an action stimulation of organism The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-1 production interleukin-1 production Drosophila teissieri Drosophila teissieri http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241 PERSON:Daniel Schober Bruker AC series NMR instrument Bruker AC series NMR instrument A series of older Bruker NMR magnets, now out of production. GROUP:<http://msi-ontology.sourceforge.net> removing CD4+ cells from PBMCs using magnetic beads. isolation of cell population isolation of cell population bp is a process in which a population of cells with certain characteristics is isolated from a larger population vital dye role vital dye role Jennifer Fostel Bombycoidea Bombycoidea IEDB immunogen role immunogen role IEDB any entity capable of eliciting an immune response when introduced to components of the immune system Muridae Muridae PERSON: Jennifer Fostel A planned process which results in physical changes in a specified input material material transformation material processing PERSON: Philippe Rocca Serra PERSON: Frank Gibson PERSON: Bjoern Peters OBI branch derived A cell lysis, production of a cloning vector, creating a buffer. PERSON: Melanie Courtot material processing Archaeoglobi Archaeoglobi Halobacteriaceae Halobacteriaceae Cricetinae Cricetinae Gadus morhua Gadus morhua John Quinn 530/30 BP filter, 585/42 BP filter band pass filter band pass filter A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others. http://en.wikipedia.org/wiki/Band_pass_filter Rhabditoidea Rhabditoidea PERSON:Daniel Schober vial vial GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117 A vial is a cylindrical container often made from glass tubing. Hypocreaceae Hypocreaceae study subject role OBI Subject study subject role inheres in an entity and realized through the execution of a study design in which the entity participates by being that which the results are about. GROUP: Role Branch Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example people infected, then extract parasite which are then tested = observation study of the parasite 1 study in which we observe people and 1 study in which subject is parasite is one way to split this. the true definition will come from the study design specification. study subject role Drosophila erecta Drosophila erecta A T cell epitope specific cytokine production assay that measures production of IL-IFNg by T cells utilizing the ELISPOT methodology. IEDB IEDB T cell epitope ELISPOT IFN-g assay T cell epitope ELISPOT IFN-g assay Ustilaginomycetidae Ustilaginomycetidae PERSON: Richard Scheuermann subgraph modularity calculation subgraph modularity calculation Richard Scheuermann A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity. CD4-positive, alpha-beta T cell CD4-positive, alpha-beta T cell A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. Pyrococcus horikoshii Pyrococcus horikoshii hospital hospital http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n A medical organization at which sick or injured people are given clinical care modified from the wording of the wordnet definition Person:Helen Parkinson human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660] Person:Alan Ruttenberg clonal cell culture a clonal cell culture is a cell culture in which all cells can be assumed to be identical, tracking back to a single ancestor cell. clonal cell culture PERSON: Susanna Sansone cell cut Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557 GROUP: OBI Biomaterial Branch Monacrosporium haptotylum Monacrosporium haptotylum Rubiaceae Rubiaceae Pill consisting of inert materials Jennifer Fostel 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 and which is physically similar in appearance to the test substance placebo role placebo role IEDB IEDB T cell epitope (3H-Thymidine) cell proliferation assay T cell epitope (3H-Thymidine) cell proliferation assay T cell epitope specific proliferation assay that measures T cell proliferation utilizing the Thymidine incorporation assay. Sinorhizobium Sinorhizobium Geospiza Geospiza Rickettsieae Rickettsieae pathogen release in laboratory accident IEDB a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent IEDB pathogen release in laboratory accident Yersinia Yersinia a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely living in endemic area IEDB IEDB living in endemic area gas chromatography detector PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> gas chromatography detector A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083 FID Corynebacteriaceae Corynebacteriaceae Listeriaceae Listeriaceae Bartonella quintana Bartonella quintana NTP-2000 is a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents Jennifer Fostel, Bjoern Peters NTP-2000 NTP-2000 Archosauria Archosauria A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample. Kevin Lister OBI fluorometer Allyson Lister fluorometer laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300 Drosophilina Drosophilina A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. PERSON:Daniel Schober variable wavelength detector variable wavelength detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079 GROUP:<http://msi-ontology.sourceforge.net> Burkholderia mallei Burkholderia mallei James Malone PERSON: Ryan Brinkman Ryan Brinkman Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry. PERSON: Richard Scheuermann gating gating PERSON:Melanie Courtot Richard Scheuermann Josef Spidlen Melanie Courtot PERSON: James Malone PERSON: Josef Spidlen Vibrio cholerae Vibrio cholerae Batrachia Batrachia PERSON: James Malone classified data set PERSON: Monnie McGee data set with assigned class labels A classified data set is a data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. classified data set Aquificae (class) Aquificae (class) Populus trichocarpa Populus trichocarpa PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months. Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group exclusion rule an exclusion rule (criterion) is_a *eligibility rule* prospective subjects should not meet to be eligible for participation in a study exclusion rule PRS Sulfolobales Sulfolobales isolation of cell culture supernatant isolation of cell culture supernatant OBI branch derived PlanAndPlannedProcess Branch Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube. a protocol which results in the separation of supernatant material from a cell culture This does not apply to the case where the cells are lysed Bill Bug Frank Gibson signal conversion function Daniel Schober Melanie Courtot A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon. signal conversion function Bifidobacteriaceae Bifidobacteriaceae Epsilonproteobacteria Epsilonproteobacteria non-negative matrix factorization Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix. Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero. http://en.wikipedia.org/wiki/Non-negative_matrix_factorization non-negative matrix factorization A relational spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. A relational spatial quality where on entity is located on left side of from the a another entity. left side of left side of software optimization software optimization Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. Jennifer Fostel Burkholderia thailandensis Burkholderia thailandensis Fringillidae Fringillidae Aquificaceae Aquificaceae GROUP:<http://msi-ontology.sourceforge.net> protein column protein column A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238 PERSON:Daniel Schober Escherichia coli Escherichia coli Culicini Culicini scaling objective Awaiting English definition from Monnie McGee scaling objective James Malone manufacturer role Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. manufacturer role Schizosaccharomyces Schizosaccharomyces Rasborinae Rasborinae whole organism preparation whole organism preparation putting a mouse in the blender. Not: putting a mouse on a scale does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged. A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained OBI branch derived hypothesis generating investigation hypothesis generating investigation is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis PlanAndPlannedProcess Branch Methylophilaceae Methylophilaceae infectious agent infectious agent IEDB is a material entity bearing the disposition to infect an organism IEDB Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome. WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant analysis Tina Hernandez-Boussard discriminant analysis Epstein Barr virus transformed B cell PERSON: Susanna Sansone Epstein Barr virus transformed B cell PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8. A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity GROUP: OBI Biomaterial Branch Kevin Clancy, Bjoern Peters restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector. restriction enzyme based cloning restriction enzyme based cloning Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages. Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488 When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium. PlanAndPlannedProcess Branch establishing cell culture OBI branch derived establishing a cell culture is a process which results in creating an in vitro environment in which cells are sustained from input material containing cells. input: cell-containing material, output cell culture, part of cell culturing. Cells are originally plated at a certain concentration referred to as seeding density. establishing cell culture Thermoproteales Thermoproteales t cell epitope prediction A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope. t cell epitope prediction PERSON: Helen Parkinson Helen Parkinson Oenococcus Oenococcus OBI PA trypsination trypsination Philippe Rocca-Serra The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483 trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity Herdmania Herdmania PERSON: Philippe Rocca-Serra Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic). PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes. phosphate buffered saline solution WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline phosphate buffered saline solution PBS buffer PERSON: Tina Boussard PERSON: Melanie Courtot Entomobryoidea Entomobryoidea Actinomyces naeslundii Actinomyces naeslundii Melanie Courtot Bill Bug heat function A heat function is a function that increases the internal kinetic energy of a material heat function Daniel Schober Frank Gibson A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. loess group transformation one-channel loess group transformation one-channel Elisabetta Manduchi A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. OTHER: Editor's generalization based on MGED Ontology term Homobasidiomycetes Homobasidiomycetes Schistosoma Schistosoma simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure http://en.wikipedia.org/wiki/Resampling_%28statistics%29 jackknifing jackknifing method Helen Parkinson jackknifing method Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method Eurotiomycetes Eurotiomycetes Melanie Courtot spectrophotometer spectrophotometer Trish Whetzel A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance. MO Helios Gamma Spectrophotometer Borrelia Borrelia Heteroderinae Heteroderinae PERSON: Philippe Rocca-Serra This includes a single scientist making a processed material for personal use. PERSON: Frank Gibson manufacturing Manufacturing implies reproducibility and responsibility AR PERSON: Bjoern Peters GROUP: OBI PlanAndPlannedProcess Branch manufacturing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process PERSON: Melanie Courtot PERSON: Jennifer Fostel Hypocreomycetidae Hypocreomycetidae Sauria Sauria PERSON: James Malone James Malone, Helen Parkinson error correction objective Application of a multiple testing correction method An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. error correction objective Homo Homo Gammaproteobacteria Gammaproteobacteria CytoSence CytoSence John Quinn A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites. http://www.cytobuoy.com/ Linum usitatissimum Linum usitatissimum hypothesis test objective James Malone statistical hypothesis test objective statistical hypothesis test objective Bruker Efficient Sample Transfer NMR http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206 Bruker BEST NMR system PERSON:Daniel Schober Bruker BEST NMR system The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. WEB:<http://www.bruker-biospin.com/automation.html> Thermotoga Thermotoga Diptera Diptera Dictyosteliida Dictyosteliida person:Chris Stoeckert group:OBI An investigation report is a report on the results of an investigation. investigation results report investigation results report Acquiring 50 C57BL/6 mice in the investigators animal facilities. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI. object acquisition object acquisition Bjoern Peters, Alan Ruttenberg IEDB an object acquisition is an acquisition of an object from an investigator, institution or vendor. Participant roles include source, destination, carrier, container, transaction record, payer... Bjoern is concerned that information such as model number and serial number are to be associated with the process. Others contend that these are associated, perhaps as labels, to the instances that are the participants. Vibrionales Vibrionales Helicobacter Helicobacter Macaca fascicularis Macaca fascicularis Pseudomonas fluorescens Pseudomonas fluorescens DNA methylation profiling is a process which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion. DNA methylation profiling Philippe Rocca-Serra DNA methylation profiling OBI branch derived Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J. Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979 Sylvia Sylvia http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf John Quinn LSR2 at TSRI Flow Cytometry Core Facility A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use. LSR2 LSR2 Moorella Moorella Pecora Pecora measuring glucose concentration in blood serum measuring glucose concentration in blood serum sample population PERSON: Jennifer Fostel PERSON: Philippe Rocca-Serra recruited population sample population GROUP: OBI Biomaterial Branch A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers. Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458 Spirochaetes (class) Spirochaetes (class) Paxillaceae Paxillaceae melanogaster group melanogaster group Aspergillus niger Aspergillus niger Cannabis sativa Cannabis sativa Taeniopygia Taeniopygia fluorescently labeled MHC multimer fluorescently labeled MHC multimer A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand group:OBI person:Chris Stoeckert quantitative confidence value quantitative confidence value A quantitative confidence value is a information content entity which is used to indicate the degree of uncertainty about a measurement. Ehrlichia Ehrlichia Plasmodium falciparum Plasmodium falciparum Obtectomera Obtectomera Hominoidea Hominoidea Leuconostoc mesenteroides Leuconostoc mesenteroides This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription synthesize synthesis synthesis making cDNA from nucleotides using RNA as a template OBI branch derived the construction of a biomaterial from simpler biomaterials PERSON:Kevin Clancy Campylobacteraceae Campylobacteraceae Sub-investigator is a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline sub-investigator role sub-investigator role Jennifer Fostel Bombyx Bombyx Aspergillus terreus Aspergillus terreus Enterobacteriaceae Enterobacteriaceae http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108 GROUP:<http://msi-ontology.sourceforge.net> PERSON:Daniel Schober A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column. plunger column plunger column Bacillus Bacillus Thermotogales Thermotogales Filarioidea Filarioidea Philippe Rocca-Serra immobilization immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum. PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23. OBI-Branch immobilization Magnetospirillum magnetotacticum Magnetospirillum magnetotacticum Entomoplasmatales Entomoplasmatales Craniata Craniata drug added to a buffer contained in a tube; substance injected into an animal; OBI material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process material to be added role Role Branch material to be added role Jennifer Fostel role of pathology review board role of pathology review board Pathology review board is a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation pseudomallei group pseudomallei group Suina Suina edge quality calculation PERSON: Richard Scheuermann A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network. edge quality calculation Richard Scheuermann Solanaceae Solanaceae Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm role of being consumer safety officer OBI, CDISC role of being consumer safety officer Jennifer Fostel Person charged with serving as CSO, FDA official who coordinates the review gamma counter gamma counter A processed material which measures gamma radiation http://en.wikipedia.org/wiki/Gamma_counter A Geiger counter Frank Gibson The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-1 beta production interleukin-1 beta production Oryzeae Oryzeae Nicotiana Nicotiana Vicieae Vicieae Bartonella Bartonella IEDB living with infected household contact living with infected household contact a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent IEDB Trichodesmium erythraeum Trichodesmium erythraeum Caulobacter vibrioides Caulobacter vibrioides flame ionization detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197 A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample. PERSON:Daniel Schober WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> flame ionization detector FID blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. a role borne by a material entity that is gained during a specimen creation process and that is realized by use of the specimen in an investigation parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. specimen role OBI liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. specimen role GROUP: Role Branch 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance calibration substance role calibration substance role Jennifer Fostel pH buffer used to calibrate a pH meter bears a calibration substance role injection function The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc. PERSON: Alan Ruttenberg adapted from WEB: http://www.dictionary.net/injection PERSON: Melanie Courtot injection function This class is temporary and will be placed outside of data transformation ultimately (if it still remains at all after review) mathematical feature PERSON: James Malone feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation mathematical feature James Malone IEDB T cell epitope (BrdU) cell proliferation assay IEDB T cell epitope specific proliferation assay that measures T cell proliferation utilizing the BrdU incorporation assay. T cell epitope (BrdU) cell proliferation assay Clostridium Clostridium PERSON:Daniel Schober A cation exchange column is a chromatography column that is used in cation exchange chromatography. GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096 cation exchange column cation exchange column Apidae Apidae mononuclear cell mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form. Anabaena Anabaena PERSON: Daniel Schober A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions. The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions. Daniel Schober protein microarray protein microarray IEDB A T cell epitope specific cytokine production assay that measures production of IL-13 by T cells utilizing the ELISPOT methodology. T cell epitope ELISPOT IL-13 assay IEDB T cell epitope ELISPOT IL-13 assay mitosporic Saccharomycetales mitosporic Saccharomycetales Student's t-test WEB: http://en.wikipedia.org/wiki/T-test Student's t-test Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value. James Malone OBI The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm Jennifer Fostel reporting party role reporting party role Reporting party role is a study personnel role played by a party who reports the outcome of a study component Frank Gibson Daniel Schober http://en.wikipedia.org/wiki/Mechanical_work mechanical function Bill Bug mechanical function A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force. Melanie Courtot Macaca mulatta Macaca mulatta BioSorter2000 BioSorter2000 A BioSorter2000 is a 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 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter. John Quinn http://www.unionbio.com/products/BioSorter.html BioSorter 2000 at TSRI Flow Cytometry Core Facility Monnie McGee data imputation Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm. ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. data imputation Philippe Rocca-Serra OBI Instrument needle needle a needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture. Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature. Diagn Cytopathol. 2008 Oct 16. PMID: 18925569 Gadus Gadus compliance rule a compliance rule is a rule which ensures a compliance process occurs compliance rule PRS PRS Eumalacostraca Eumalacostraca WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores. principal component regression Tina Hernandez-Boussard principal component regression Streptococcus pneumoniae Streptococcus pneumoniae fluorescene detector fluorescene detector http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080 WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html> A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected. PERSON:Daniel Schober Macaca Macaca Ctenosquamata Ctenosquamata Burkholderia cepacia complex Burkholderia cepacia complex http://www.guavatechnologies.com/main/products/easyCyteMini.cfm A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement. Guava EasyCyte Mini Guava EasyCyte Mini John Quinn Lycopersicon Lycopersicon PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106 reversed phase column reversed phase column A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column. epitope specific IL-2 release by T cells epitope specific IL-2 release by T cells IEDB IEDB A biological process where T cells produce IL-2 resulting from the recognition of a T cell epitope. Candida Candida Cyprinoidea Cyprinoidea occurrence of infectious disease IEDB Is an occurrence of a disease caused by an infection IEDB occurrence of infectious disease eurosids II eurosids II 500, 200, 0 number of particles in subset A number of particles in subset is a datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of particles in subset person:Kevin Clancy Strongyloides Strongyloides Clostridium botulinum Clostridium botulinum Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 John Quinn Rhodamine 101 dye laser used to irradiate cells in a flow cytometer. dye laser Daniel Schober A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification. dye laser Bifidobacterium Bifidobacterium Solanum tuberosum Solanum tuberosum Strigeidida Strigeidida sample inlet sample inlet PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044 WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets> The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head. Vertebrata Vertebrata A40-MiniFCM A40-MiniFCM A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus. John Quinn http://www.apogeeflow.com/flow_cytometry_products.htm Coccidia Coccidia interleukin-5 production interleukin-5 production The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. PERSON: Monnie McGee Monnie McGee interquartile-range calculation interquartile-range calculation The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data. Drosophiliti Drosophiliti A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through Frank Gibson filter function filter function WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. PERSON: Chris Stoeckert dependent variable specification PERSON: Alan Ruttenberg dependent variable specification PERSON: Bjoern Peters dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. The prothrombin time is an assay most commonly measured using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant by binding the calcium in a sample. The blood is mixed, then centrifuged to separate blood cells from plasma. In newborns, whole blood is used. The plasma is analyzed by a biomedical scientist on an automated instrument at 37 degrees C, which takes a sample of the plasma. An excess of calcium is added (thereby reversing the effects of citrate), which enables the blood to clot again. For an accurate measurement the proportion of blood to citrate needs to be fixed; many laboratories will not perform the assay if the tube is underfilled and contains a relatively high concentration of citrate. If the tube is underfilled or overfilled with blood, the standardized dilution of 1 part anticoagulant to 9 parts whole blood is no longer valid. For the prothrombin time test the appropriate sample is the blue top tube, or sodium citrate tube, which is a liquid anticoagulant. Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically. Some laboratories use a mechanical measurement, which eliminates interferences from lipemic and icteric samples. The prothrombin ratio is the prothrombin time for a patient, divided by the result for control plasma. 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 PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). WEB:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 prothrombin time assay Person:Alan Ruttenberg prothrombin time assay A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer. Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 generalized family wise error rate correction method generalized family wise error rate correction method gFWER correction Monnie McGee Daniel Schober FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc. diode laser diode laser A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer. John Quinn separation into different composition objective separation into different composition objective The objective to obtain cells contained in a sample of blood. We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives is the objective to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities) A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations. PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101 GROUP:<http://msi-ontology.sourceforge.net> glass column glass column Ryan Brinkman Melanie Courtot James Malone log-log curve fitting ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446 log-log curve fitting A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points. Elisabetta Manduchi Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. Daniel Schober Bill Bug display function A display function is a function to present information by translating that information through some lookup process into visual form. display function Melanie Courtot Frank Gibson survival analysis data transformation survival analysis data transformation A data transformation which http://www.cytopeia.com/analyzer.htm The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells. John Quinn inFlux Analyzer inFlux Analyzer Methanosarcinales Methanosarcinales http://www.biotech.ist.unige.it/cldb/cl1597.html A cell line derived from human cervical cancer cells. HeLa cell culture HeLa cell culture IEDB IEDB Sphingobacteria Sphingobacteria ionize process ionize process paired-end tag (PET) library Philippe Rocca-Serra paired-end library mate-paired library adapted from information provided by Solid web site is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y. paired-end library cytological stain role cytological stain role Jennifer Fostel Dictyostelium Dictyostelium Reagent role is a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances GROUP: Role Branch reagent role www.answers.com/topic/reagent; November 2008 reagent role Buffer, dye, a catalyst, a solvating agent. merging of columns from two different data sets James Malone combining objective PERSON: Data Transformation Branch merging objective A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets. merging objective Corynebacterineae Corynebacterineae Burkholderiales Burkholderiales A T cell population characterized by not expressing the CD3 molecule on its surface. CD3- T cell culture CD3- T cell culture IEDB IEDB Festuca rubra subsp. littoralis Festuca rubra subsp. littoralis Bill Bug Daniel Schober An electricity cable Frank Gibson A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another. connection function Melanie Courtot connection function A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions. Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software Elisabetta Manduchi differential expression analysis objective PERSON: Elisabetta Manduchi differential expression analysis objective network analysis Richard Scheuermann network topology analysis PERSON: Richard Scheuermann A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network. network analysis nucleic acid template role is a reference role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy. nucleic acid template role a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 nucleic acid template role Orbiliomycetes Orbiliomycetes Staphylococcus Staphylococcus IEDB An assay in which a positive measurement indicates TCR recognition of an epitope:MHC context. Inputs to the assay include: 1) the assay antigen which contains the epitope, 2) TCR molecules 3) restricting MHC molecules. T cell epitope recognition assay IEDB T cell epitope recognition assay IEDB IEDB The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell. restricting MHC role restricting MHC role Isotomidae Isotomidae Amphibia Amphibia A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. regulatory agency WEB: en.wikipedia.org/wiki/Regulator The US Environmental Protection Agency GROUP: OBI Biomaterial Branch regulatory agency scattered molecular aggregate A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 the sodium and chloride ions in a glass of salt water Collective scattered molecular aggregate PERSON: Alan Ruttenberg Mus musculus Mus musculus Sulfolobus solfataricus Sulfolobus solfataricus data collection data collection Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC OBI branch derived Bjoern Peters Is an acquisition of information from an organization that provides information. This is not an assay. It consists of specifiying a query what information is desired, putting this query to an organization, and retrieveing the requested information from the organization. Rhizobium/Agrobacterium group Rhizobium/Agrobacterium group Synechocystis Synechocystis single cell gel electrophoresis assay a comet assay is an assay which utilizes gel electrophoresis on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions. SCGE assay comet assay PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review. PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra comet assay Eucoccidiorida Eucoccidiorida bp is an objective to obtain an output material that contains several input materials. PPPB branch material combination objective material combination objective Archaeoglobaceae Archaeoglobaceae Acinetobacter baumannii Acinetobacter baumannii Rhodobacteraceae Rhodobacteraceae IEDB The process of an immunogen coming into contact with a host organism. May be a natural process (occurrence or exposure) or an administration in vivo. immunization immunization IEDB Teleostomi Teleostomi Paxillus filamentosus Paxillus filamentosus campanulids campanulids A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073 WEB:<http://www.chromatography-online.org/topics/fraction/collector.html> PERSON:Daniel Schober fraction collector fraction collector The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. interleukin-4 production interleukin-4 production Enterogona Enterogona Thermobifida fusca Thermobifida fusca A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors). Elisabetta Manduchi total intensity transformation paired OTHER: Adjusted from MGED Ontology total intensity transformation paired This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays. Philippe Rocca-Serra IEDB epitope specific IL-5 release by T cells epitope specific IL-5 release by T cells A biological process where T cells produce IL-5 resulting from the recognition of a T cell epitope. IEDB double-stranded DNA double-stranded DNA GROUP: OBI Biomaterial Branch PERSON: Philippe Rocca-Serra agarose gel agarose gel Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269 agarose gel is a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution flow cytometer analyzer John Quinn An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis. http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm flow cytometer analyzer FACS Calibur, Luminex 100 Coxiella Coxiella quantile calculation WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html quantile calculation Monnie McGee A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details. histological sample preparation OBI branch derived PERSON:Bjoern Peters histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay histological sample preparation spin column spin column PERSON:Daniel Schober A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits. http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232 GROUP:<http://msi-ontology.sourceforge.net> Deinococci Deinococci health care provider role health care provider role Jennifer Fostel Healthcare provider is a worker role of providing medical care either within or outside the study timeline Callithrix jacchus Callithrix jacchus Borrelia burgdorferi Borrelia burgdorferi http://en.wikipedia.org/wiki/Glucose_meter PERSON:Frank Gibson glucometer glucometer Diabetic patients use glucometers to determine their glucose levels glucose meter PERSON:Helen Parkinson A measurement device with the function to measure and record the level/amount of glucose in a blood sample Ovis aries Ovis aries Ustilaginales Ustilaginales http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp FC 500 FC 500 A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications. John Quinn 620 SP filter short pass filter short pass filter A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm. http://en.wikipedia.org/wiki/Low-pass_filter John Quinn Cyanothece sp. ATCC 51142 Cyanothece sp. ATCC 51142 A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed' quantile number of false positives correction method quantile number 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. 19 Monnie McGee QNFP B cell epitope recognition assay is an assay that measures the binding of an epitope to an antibody or B cell receptor, or an immune response process resulting from such a binding event B cell epitope recognition assay IEDB IEDB Rickettsia prowazekii Rickettsia prowazekii PERSON:Daniel Schober http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059 GROUP:<http://msi-ontology.sourceforge.net> An Instrument which is used to carry out a NMR analysis of some sample. NMR instrument NMR instrument NMR instrument Phaeophyceae Phaeophyceae OBI branch derived experimental disease induction experimental disease induction PlanAndPlannedProcess Branch a protocol application to induce a specific disease in an organism the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome. Geospiza fortis Geospiza fortis James Malone submatrix extraction submatrix extraction Melanie Courtot A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.) WEB: http://en.wikipedia.org/wiki/Submatrix When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set. Elisabetta Manduchi Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix. divisive hierarchical clustering Elisabetta Manduchi divisive hierarchical clustering James Malone top-down hierarchical clustering PERSON: Elisabetta Manduchi A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain. Cyanobacteria Cyanobacteria PERSON: Melanie Courtot James Malone PERSON: James Malone Melanie Courtot data visualization PERSON: Elisabetta Manduchi PERSON: Tina Boussard Tina Boussard An planned process that creates images, diagrams or animations from the input data. visualization data encoding as image Generation of a heatmap from a microarray dataset Elisabetta Manduchi data visualization reverse transcriptase reverse transcriptase person:Melanie Courtot enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) group:OBI Passeriformes Passeriformes soil soil Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m. Buchnera Buchnera Gibberella Gibberella Linaceae Linaceae Nostocaceae Nostocaceae interleukin-24 production interleukin-24 production The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Holm false discovery rate correction method