en Ontology for Biomedical Investigations Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg Allyson Lister Barry Smith Bill Bug Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Chris Taylor Christian Bolling Cristian Cocos Daniel Rubin Daniel Schober Dawn Field Dirk Derom Elisabetta Manduchi Eric Deutsch Frank Gibson Gilberto Fragoso Helen C. Causton Helen Parkinson Holger Stenzhorn James A. Overton James Malone Jay Greenbaum Jeffrey Grethe Jennifer Fostel Jessica Turner Jie Zheng Joe White John Westbrook Kevin Clancy Larisa Soldatova Lawrence Hunter Liju Fan Luisa Montecchi Matthew Brush Matthew Pocock Melanie Courtot Melissa Haendel Mervi Heiskanen Monnie McGee Norman Morrison Philippe Rocca-Serra Phillip Lord Pierre Grenon Richard Bruskiewich Richard Scheuermann Robert Stevens Ryan R. Brinkman Stefan Wiemann Susanna-Assunta Sansone Tanya Gray Tina Hernandez-Boussard Trish Whetzel Yongqun He 2009-07-31 An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation. OWL-DL An ontology for the annotation of biomedical and functional genomics experiments. http://creativecommons.org/licenses/by/4.0/ Ontology for Biomedical Investigations Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. 2026-07-27 An alternative term used by the ISA tools project (http://isa-tools.org). Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term An alternative term used by the Functional Genomics Data (FGED) Society. PERSON: Chris Stoeckert, Jie Zheng Penn Group FGED alternative term Contributor Coverage Creator Date Description Format Resource Identifier Language Publisher Relation Rights Management Source Subject and Keywords Title Resource Type Mark Miller 2018-05-11T13:47:29Z label The provides_service_consumer_with relation links the service to its primary process it provides for the consumer (as opposed to secondary processual parts of a service process such as payment or documentation). For example, a 'DNA sequencing service' provides_service_consumer_with 'DNA sequencing' as the essential process performed by the provider for the client. A relation between a service and the primary processual part of the service that is performed by the provider for the consumer. provides_service_consumer_with The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has specified input see is_input_of example_of_usage The inverse property of is specified input of 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has specified input is_concretization_of Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. replaced by: http://purl.obolibrary.org/obo/BFO_0000058 PERSON: Alan Ruttenburg PERSON: Barry Smith obsolete_is_concretization_of true is specified input of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a completely executed planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified input of is_concretized_as Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. replaced by: http://purl.obolibrary.org/obo/BFO_0000059 PERSON: Alan Ruttenberg PERSON: Barry Smith obsolete_is_concretized_as true has_quality A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm] replaced by: http://purl.obolibrary.org/obo/BFO_0000086 GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall obsolete_has_quality true has specified output The inverse property of is specified output of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has specified output is_realized_by Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] replaced by http://purl.obolibrary.org/obo/BFO_0000054: 'is realized by' GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall executed_during has_realization is_realized_as obsolete_is_realized_by true obsoleted_has_specified_output_information A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data. PERSON: Alan Ruttenberg PERSON: Frank Gibson obsoleted_has_specified_output_information true is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan has_make has_manufacturer is_manufactured_by has_function heart has_function to-pump-blood Relation between an independent continuant and a function. replaced by: http://purl.obolibrary.org/obo/BFO_0000085 GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall obsolete_has_function true obsoleted_is_reagent_in some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole Alan Ruttenberg obsoleted_is_reagent_in true realizes example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes. Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm] replaced by http://purl.obolibrary.org/obo/BFO_0000055: 'realizes' GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungal executes has_function_part involves_execution_of is_realization_of obsolete_realizes true obsoleted_utilizes_reagent see example_of_usage for is_reagent_in Relationship between a protocol application and a substance that has role reagent that participates in the protocol application Alan Ruttenberg obsoleted_utilizes_reagent true obsoleted_is_device_for some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay Relationship between a device and a protocol application in which it participates Alan Ruttenberg obsoleted_is_device_for true is specified output of A relation between a completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is specified output of obsoleted_utilizes_device see example_of_usage for is_device_for Relationship between protocol application and an intrument in which it participates Alan Ruttenberg obsoleted_utilizes_device true is_proxy_for position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be. A relation between continuant instances c1 and c2 where within a protocol application, measurement of c1 is related to a what would be the measurement of c2. (another definition) Alan Ruttenberg is_proxy_for has specified input information A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data. PERSON: Frank Gibson PERSON:Alan Ruttenberg consumes data obsoleted_has_specified_input_information true has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. replaced by: http://purl.obolibrary.org/obo/BFO_0000087 GROUP:OBI:<http://obi.sourceforge.net> PERSON:Chris Mungal obsolete_has_role true obsolete_results_from 2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178 . Should be replaced by instead creating defined classes for materials, which are specified output of the process that conveys the obsolete_results_from true achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective is_specified_information_output_of A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation. is replaced by has_specified_output_of PERSON: James Malone Editor obsoleted_is_specified_information_output_of true has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain obsoleted_is_specified_information_intput_of Is the inverse relation of has_specfied_input_information is replaced by is_specified_intput_of obsoleted_is_specified_information_intput_of true is grain of A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole. JAO: Added definition 2013-10-25 based on 'has grain', but both these terms seem problematic. PERSON: Alan Ruttenberg 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 is grain of provisions A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use 5/11/2020: A prior definition contained reference to transfer of ownership. ("A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner"). This was left out as it was hard to read and it was unclear if/how that transfer restricts the relationship. GROUP: Relations branch supplies provisions has_supplier A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner. PERSON: Alan Rutternberg PERSON: Cristian Cocos PERSON: Frank Gibson PERSON: Melanie Courtot has_supplier objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by is member of organization Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it. Person:Alan Ruttenberg Person:Helen Parkinson Person:Alan Ruttenberg Person:Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case is member of organization has category label A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale. has category label has disposition to bind A relationship between two material entitites that each have disposition to form a complex with the other. This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other IEDB has disposition to bind Relating an organization to a legal person or organization. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 Person: Jie Zheng has organization member A relation between a value specification and an entity which the specification is about. specifies value of A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process. OBI OBI The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). has performer A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc. Hector Guzman-Orozco OBI https://github.com/obi-ontology/obi/issues/1516 has assay target context has study design A relation between an investigation and a study design in which part of the investigation is a study design execution that carries out the study design. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1831 Charlie Hoyt has study design is study design of A relation between a study design and an investigation when part of the investigation is a study design execution that carries out the study design. Sebastian Duesing https://github.com/obi-ontology/obi/issues/1831 Charlie Hoyt is study design of process is result of The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR is a relationship between a process and a preceding occurrent that directly caused the later one to occur IEDB PERSON:Bjoern Peters process is result of is_described_by obsolete_is_described_by true bound_to A relationship between two material entities that form a complex based on a selective, non-covalent interaction. The definition of this term is modeled after the Chebi:50967 and GO:0005488 terms. Further alignment of the logical definitions with those ontologies will require agreement on the placement of GO:molecular function in BFO among other things. OBI will retire this term once such an alignment is achieved as 'bound to' is not in the primary OBI scope. bound_to adjacent to has_feature_value has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values. James Malone has_feature_value A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI has specified numeric value A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value 12th arrondissement of Paris 20g I feel sick to my stomach every Tuesday 'has representation' is a data property that attaches between an information content entity and a value that contains linguistically or computationally coded text. Further processing may enable the value to be represented in a component data structure such as an OBI value specification. Damion Dooley Mark Miller 2019-07-14T07:05:50Z has representation polymer Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores. FM fluorescence imaging fluorescence microscopic imaging CHMO fluorescence microscopy assay Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence. CLSM LSCM confocal fluorescence imaging confocal laser scanning fluorescence microscopy confocal laser scanning microscopy confocal-laser scanning microscopy fluorescence confocal microscopy fluorescence confocal scanning laser microscopy scanning confocal fluorescence microscopy CHMO confocal fluorescence microscopy assay Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image. OM light microscopy optical microscopy CHMO light microscopy assay A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series. LC-MS-MS LC-MS/MS LC-MS2 LC-MSMS LC/MS/MS LCMSMS liquid chromatography tandem mass spectrometry liquid chromatography tandem mass spectroscopy liquid chromatography-tandem mass spectroscopy CHMO liquid chromatography-tandem mass spectrometry 'derives from' is transitive, so even cell line cells created through modification of an existing cell line cell have derived_from some initial primary cultured cell that existed at some point in time. 0 PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." TNF alpha production TNF beta production A ribosome is a protein complex. protein complex antibody antibody human being role of being consumer safety officer Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm Person charged with serving as CSO, FDA official who coordinates the review the role of a human being that is realized by enforcing regulations to ensure consumer safety Jennifer Fostel Person:Helen Parkinson OBI, CDISC role of being consumer safety officer fluorescent reporter intensity A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter. person:Chris Stoeckert group:OBI From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem. fluorescent reporter intensity Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) obsolete planned process true regulator role 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 a regulatory role involved with making and/or enforcing relevant legislation and governmental orders Person:Jennifer Fostel regulator OBI regulator role 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 regulation-assigned role Approval letter Regulation-assigned role is a regulatory role defined by legislation or governmental orders Person: Jennifer Fostel regulation-assigned role regulatory role Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 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. GROUP: Role branch OBI, CDISC govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent regulatory role material supplier role Jackson Labs is an organization which provide mice as experimental material a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. Supplier role is a special kind of service, e.g. biobank PERSON:Jennifer Fostel material provider role supplier material supplier role contract research organization role a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution Person: Jennifer Fostel contract research organization contract research organization role list-mode data file An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used. A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter. One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people. person:Chris Stoeckert group:Flow Cytometry community list-mode data file classified data set 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. PERSON: James Malone PERSON: Monnie McGee data set with assigned class labels classified data set reference substance role 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 a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. Person:Jennifer Fostel reference substance OBI reference substance role cytological stain role haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization Person:Helen Parkinson Person:Jennifer Fostel cytological stain cytological stain 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 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.. GROUP: Role branch OBI 9Mar09 after discussion with process branch changed definition to include use of centrifuge; centrifuge pellet role clinical research coordinator role a worker role comprised of handling the administrative duties of a trial or study. Person:Jennifer Fostel clinical research coordinator clinical research coordinator role supernatant role 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 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. GROUP: Role branch OBI supernatant role chromatography column Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms. Frank Gibson http://en.wikipedia.org/wiki/Column_chromatography open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 chromatography column drug role http://www.answers.com/topic/drug 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act. a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism Role Branch drug OBI, CDISC drug role pump valve switch A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow. FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument OBI Instrument branch OBI pump valve switch xenotransplantation is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans PlanAndPlannedProcess Branch OBI branch derived xenotransplantation physical document a book is a physical document A physical document is an object serving as a record of information by means of symbolic marks. PERSON: Bjoern Peters GROUP: OBI physical document waiting A planned process where an agent does not take any new actions towards a particular objective for a period of time until a set of conditions is met. PERSON:Alan Ruttenberg OBI branch derived BP: I have doubts about the utility of this. We need a better handling/modeling of time (January 2008) waiting Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg obsolete processed material true chromatography device 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. Frank Gibson chromatography instrument http://en.wikipedia.org/wiki/Chromatography open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178 chromatography device mass spectrometer LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific 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 Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry mass spectrometer A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI. OBI Instrument branch OBI Instrument branch obsolete_platform true liquid chromatography mass spectrometry platform A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI. OBI instrument branch OBI Instrument branch liquid chromatography mass spectrometry platform microarray platform 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 ratio of collected to emitted light 10% A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role person:Chris Stoeckert person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt ratio of collected to emitted light software optimization objective Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software. Jennifer Fostel software optimization objective notified body role The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf 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 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. Person: Jennifer Fostel notified body OBI, CDISC notified body role allotransplantation is the transplantation of organs between members of the same species. PlanAndPlannedProcess Branch OBI branch derived allotransplantation gamma counter A Geiger counter A processed material which measures gamma radiation Frank Gibson http://en.wikipedia.org/wiki/Gamma_counter gamma counter trial monitor role a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study Person:Jennifer Fostel trial monitor CDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study. trial monitor role positive reference substance role MMS mutagen a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response Person: Jennifer Fostel positive reference substance positive reference substance role 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. 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 Philippe Rocca-Serra adapted from Wikipedia before possible import from CHEBI polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding achieves objective of drawing conclusion as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study investigation evaluant role When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source. a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is) examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. evaluant role reporting party role Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress. 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 a study personnel role played by a party who reports the outcome of a study component MO:submitter mapped to this term. So, alternative term 'submitter' was added. Jennifer Fostel reporting party submitter OBI reporting party role assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay quantitative confidence value A data item which is used to indicate the degree of uncertainty about a measurement. person:Chris Stoeckert group:OBI quantitative confidence value sample preparation for assay A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. PlanAndPlannedProcess Branch study OBI branch derived sample preparation for assay diagnosis textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. Jennifer Fostel diagnosis textual entity 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. PERSON: Bjoern Peters OBI unplanned occurrence effecting an investigation eMedical record An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11. person:Jennifer Fostel article-without-pmid-or-doi:CDISCglossary eMedical record culture medium A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ. Person: Jennifer Fostel, Jie Zheng OBI culture medium electronic case report tabulation 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. person:Jennifer Fostel CDISC glossary electronic case report tabulation polystyrene tube Polystyrene tubes can be used to contain tissue culture cells during centrifgation A polystyrene tube is a test tube made of polystyrene PERSON: Chris Stoeckert PERSON: Chris Stoeckert polystyrene tube reagent role Buffer, dye, a catalyst, a solvating agent. A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer. PERSON:Matthew Brush reagent PERSON:Matthew Brush Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction. (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent role 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 a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture Person: Jennifer Fostel regulator of chemical manufacture OBI role of regulator of chemical manufacturer detector reagent role a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus. 19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009 detector reagent role role of certified IRB professional CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA Person:Helen Parkinson Person:Jennifer Fostel certified IRB professional WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional role of certified IRB professional 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 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 See also OMRSE:00000011 'patient role' GROUP:Role Branch patient OBI, CDISC CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably patient role A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra OBI branch derived obsolete material processing true 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 protocol testing objective study subject role 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 are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake. A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected. A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation. GROUP: Role Branch OBI Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS participant under investigation role Rat 1A; first enrolled patient to receive treatment 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 Role Branch OBI obsolete_role of being first subject treated true measured expression level Examples are quantified data from an expression microarray experiment, PCR measurements, etc. A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts. person:Chris Stoeckert OBI Data Transformation branch measured expression level responsible party role 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 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 Person: Jennifer Fostel responsible party OBI responsible party role principal investigator role a responsible party role played by a person responsible for the overall conduct of a study Person: Jennifer Fostel principal investigator CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC) principal investigator role transplantation a protocol application to replace an organ or tissue of an organism PlanAndPlannedProcess Branch OBI branch derived transplantation 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280 a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission. GROUP: Role Branch OBI and Wikipedia obsolete biological vector role true pH indicator dye role bromophenol blue has a pH indicator dye role phenol red in RPMI; pH=4 indicator dye (also carries reference role) the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity Person: Jennifer Fostel Person:Helen Parkinson pH indicator dye pH indicator dye role specimen role 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. A role borne by a material entity that is obtained during a specimen collection process and that can be realized by performing measurements or observations on the specimen. 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. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. 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. 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. GROUP: Role Branch OBI specimen role sequence feature identification objective Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. Jennifer Fostel sequence feature identification objective intervention design PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. Philppe Rocca-Serra OBI branch derived intervention design worker role Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study Person:Jennifer Fostel worker OBI worker role An assay where the output data is a datum with one of two values denoting success and failure. PlanAndPlannedProcess Branch OBI branch derived Bernoulli trial gene list 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. A data set 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. person:Chris Stoeckert group:OBI kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object. gene list number of particles in subset 500, 200, 0 A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of particles in subset number of lost events electronic 74, 0, 14 events lost due to data acquisition electronic coincidence. A measurement 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. person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events electronic calibration substance role pH buffer used to calibrate a pH meter bears a calibration substance 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 Jennifer Fostel calibration substance role molecular feature identification objective Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications. Jennifer Fostel molecular feature identification 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 hardware testing objective incubator Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled Frank Gibson http://www.medterms.com/script/main/art.asp?articlekey=18426 incubator Label role is a role which inheres in a material entity and which is realized in a detection of label assay Role Branch label OBI obsolete_label role true baseline participant role Subject at time = 0; subject before a stress test. a reference participant role which is realized by making the reference to qualities at the start of the study or intervention Person: Jennifer Fostel baseline participant baseline participant role role of independent data monitoring committee a trial monitor role charged recommending whether to continue, modify, or end the trial Person: Jennifer Fostel independent data monitoring committee role of independent data monitoring committee pathologist role a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline Person:Jennifer Fostel Pathologist pathologist role supernatant collection system harvesting frame A device that 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 filter paper A device manufacture with the intent to provide a porous unsized paper used for filtering. Frank Gibson sep:00107 filter paper 2 cell co-culturing Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. PlanAndPlannedProcess Branch OBI branch derived cell co-culturing role of Institutional Review Board 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 Animal protocol review board the role of a organization that is realized by members reviewing study designs for their agreement with regulations Person:Helen Parkinson Person:Jennifer Fostel Internal Review Board OBI, CDISC CDISC definition: institutional review board; independent ethics committee (IEC). An independent body (a review board or a committee, institutional, regional, national, or supranational) constituted of medical/scientific professionals and non-scientific members, whose responsibility it is to ensure the protection of the rights, safety and well-being of human subjects involved in a trial. role of Institutional Review Board 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 person:Jennifer Fostel article-without-pmid-or-doi:CDISCglossary eSource document crossover population role a role realized when a participant serves as reference to itself Person: Jennifer Fostel crossover population crossover population role complete nutrient role Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment. Person: Jennifer Fostel complete nutrient complete nutrient role radiolabel role a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection Jennifer Fostel radiolabel radiolabel role cDNA library PMID:6110205. collection of cDNA derived from mouse splenocytes. 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. PERSON: Luisa Montecchi PERSON: Philippe Rocca-Serra GROUP: PSI PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction clonal cDNA library electronic case report form 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 CDISC glossary electronic case report form placebo role Pill consisting of inert materials a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance Person:Jennifer Fostel placebo CDISC definition placebo. A pharmaceutical preparation that does not contain the investigational agent. In blinded studies, it is generally prepared to be physically indistinguishable from the preparation containing the investigational product. placebo role autotransplantation is the transplantation of tissue from one part of \nthe body to another in the same individual. ) PlanAndPlannedProcess Branch OBI branch derived autotransplantation parameter threshold 0.01, 0.03 A measurement 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 person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt parameter threshold study group role The group of randomized participants that are assigned to a treatment arm of the trial a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol Jennifer Fostel study group population study group role p-value PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2). A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. May be outside the scope of OBI long term, is needed so is retained PERSON:Chris Stoeckert WEB: http://en.wikipedia.org/wiki/P-value p-value population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ PERSON: Philippe Rocca-Serra adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process population Determining the binding of epitope-specific nanobody cAb-HuL5 to wild type human lysozyme by chemical shift perturbations in NMR spectra (Erwin De Genst, J Phys Chem B 2013). A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample. IEDB PlanAndPlannedProcess Branch IEDB NMR 3D molecular structure determination assay An assay that produces a picture of an entity. PlanAndPlannedProcess Branch OBI branch derived imaging assay protocol optimization objective 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 objective role of pathology review board a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation Person: Jennifer Fostel pathology review board role of pathology review board microtiter plate A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA) A microtiter_plate is a flat plate with multiple wells used as small test tubes. Melanie Courtot microplate http://en.wikipedia.org/wiki/Microtiter_plate microtiter plate role of impartial witness According to GCP , an impartial witness should be present for an illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial impartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and who Person: Helen Parkinson Person: Jennifer Fostel impartial witness role of impartial witness Yang et al, Int J Clin Exp Pathol. 2015; 8(3): 2746–275 PMID:26045780. Cells were lysed and sonicated to shear DNA to lengths between 200-1000 bp. The sample was then incubated with antibodies against Acety-H3 to immunoprecipitate protein-DNA complexes using protein A agarose beads. The isolated protein-DNA complexes were treated with proteinase K digestion to remove histones. QPCR was then performed using primers specific for TGF-β1, MMP-9 and PI3K promoters at 95°C for 5 min, followed by 40 cycles at 95 °C for 20 s, 58°C for 20 s, and 72°C for 20 s. Each QPCR reaction was repeated in triplicate. QPCR was followed by a melt curve analysis to determine the reaction specificity. The relative gene expression was calculated using 2-ΔΔCt method. An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics. Bjoern Peters, Randi Vita, James A. Overton ChIP OBI chromatin immunoprecipitation biological replicate role A member of a dose-time group; a patient in a given arm of a trial a reference participant role realized by equivalent treatment of participants Person:Jennifer Fostel biological replicate OBI biological replicate role Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material. An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material. IEDB PlanAndPlannedProcess Branch IEDB radioactivity detection investigation agent role The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing. Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen. Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable representing investigations run by robot scientists such as ADAM (King et al, Science, 2009) GROUP: Role Branch investigator OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. study person role Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) investigation agent role nutrient role 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 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. GROUP: Role branch nutrient Wikipedia, feb 29, 2008 19 Feb 2009; old def: A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment. nutrient role 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) 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. Role Branch OBI obsolete_dropout role true a worker role of providing medical care either within or outside the study timeline Person:Jennifer Fostel health care provider obsolete health care provider role true methodology testing objective Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies. Jennifer Fostel methodology testing objective analytical cytology data file FCS file, ACS file, foo.fcs, foo.asc A digital entity intended to capture data in analytical cytology domain. person:Chris Stoeckert group:Flow Cytometry community analytical cytology data file proxy respondent role Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel Jennifer Fostel proxy respondent proxy respondent role fluorescence compensation matrix ((1.053096, -0.22476), (-0.24877, 1.053096)) A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix. person:Chris Stoeckert group:Flow Cytometry community fluorescence compensation matrix negative reference substance role Saline solution 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 Person: Jennifer Fostel negative reference substance negative reference substance role role of legally acceptable representative 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 a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial. 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] Person: Jennifer Fostel Person:Helen Parkinson legally acceptable representative OBI, CDISC role of legally acceptable representative investigation results report An investigation report is a report on the results of an investigation. person:Chris Stoeckert group:OBI investigation results report cellular feature identification objective Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation. Jennifer Fostel cellular feature identification objective reference subject role Saline treated rat; one of three identically-treated subjects a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference Jennifer Fostel reference participant OBI reference subject role vital dye role typtan blue has a vital dye A dye role that is realized when used to detect live cells in an experiment 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178 Person: Helen Parkinson Person: Jennifer Fostel vital dye vital dye role 115 patients received ipilimumab and blinded medication Inert pill shaped like aspirin tablet Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance Jennifer Fostel Person:Helen Parkinson obsolete_blinded medication role true sub-investigator role a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline Person: Jennifer Fostel sub-investigator CDISC definition: Sub-investigator. Any member of the clinical trial team designated and supervised by the investigator at a trial site to perform critical trial-related procedures and/or to make important trial-related decisions (e.g., associates, residents, research fellows) [ICH] See associates, residents, research fellows sub-investigator role data encoding storage of measurement results from an assay into a text file, such as a documenting process to encode an information entity into a digital document PlanAndPlannedProcess Branch OBI branch derived We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE data encoding enzymatic cleavage Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828 a material processing that digests the fraction of input material that is susceptible to that enzyme PlanAndPlannedProcess Branch OBI branch derived enzymatic cleavage hardware optimization objective Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. Jennifer Fostel hardware optimization objective Place holder class, Utility class to gather the defined classes Susanna Sansone OBI Biomaterial derived obsolete_defined_material true trial statistician role a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated. Person:Jennifer Fostel trial statistician CDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9] trial statistician role standard error A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution. person:Chris Stoeckert group:OBI see P-Value standard error antigen role A role of a material entity that is being recognized in whole or in part by receptors of the immune system such as antibodies or T cell receptors. 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 Role Branch OBI 9Mar09 waiting for discussion with immunology terms antigen role software testing objective Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software. Jennifer Fostel software testing objective sponsor role a responsible party role involved with any of the following activities: initiating, managing and funding a study Person: Jennifer Fostel sponsor CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators sponsor role organization 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 entity that can bear 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. 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: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization feed role 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 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. Person: Jennifer Fostel feed OBI feed role technical replicate role Aliquots of a tissue subjected to parallel assays technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay Person: Jennifer Fostel technical replicate technical replicate role dye role A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest. Jennifer Fostel dye A substance used to color materials www.answers.com/topic/dye 19feb09 dye role cluster Cluster of the lymphocytes population. A data set which is a subset of data that are a similar to each other in some way. person:Allyson person:Chris Stoeckert group:OBI cluster cohort role In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008 a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study. Jennifer Fostel WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students. WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site). WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation. cohort role artificially induced nucleic acid hybridization www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules. PlanAndPlannedProcess Branch OBI branch derived artificially induced nucleic acid hybridization DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. PlanAndPlannedProcess Branch OBI branch derived DNA extraction plan 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 completely executed planned process. 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. AR, BP, JM, MC, PRS branch derived plan 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 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. PERSON: Jennifer Fostel PERSON: Philippe Rocca-Serra recruited population GROUP: OBI Biomaterial Branch obsolete_sample population true organism feature identification objective 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. Jennifer Fostel organism feature identification objective number of lost events computer 0, 125, 787 events lost due to computer busy. A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role person:Kevin Clancy Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt number of lost events computer protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol role of regulator of consumables and medical devices FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices Person: Jennifer Fostel drug regulatoy authority OBI, CDISC role of regulator of consumables and medical devices adding a material entity into a target Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. BP branch derived adding a material entity into a target analyte role Glucose in blood (measured in an assay to determine the concentration of glucose). A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role. interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. qualities such as weight, color are not assayed but measured, so they do not fall into this category. GROUP: Role Branch OBI Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. analyte role disease stage Stage II breast cancer, The timepoint of recovery from a disease a part of an occurrence of a disease process which is associated with position in the normal progression of the disease PERSON: Bjoern peters disease stage intraperitoneal injection 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 precipitate Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038 a precipitate is a material entity which is output of a precipitation process PERSON: Philippe Rocca-Serra precipited material GROUP: OBI Biomaterial Branch precipitate An assay that determines interactions between proteins, such as protein-protein binding. protein-protein interaction detection assay Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors Philippe Rocca-Serra TF binding OBI https://sourceforge.net/p/obi/obi-terms/767/ transcription factor binding site assay Enrollment of patients in a study. Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902 enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules Bjoern Peters IEDB obsolete_enrollment true adverse event trigger revisit? PERSON:Alan Ruttenberg OBI branch derived adverse event trigger eluate Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263 a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role PERSON: Philippe Rocca-Serra eluted material OBI Bionaterial eluate material to be added role drug added to a buffer contained in a tube; substance injected into an animal; A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role is added into another material entity (the target). Role Branch OBI 9 March 09 from discussion with PA branch material to be added role is the serous membrane that forms the lining of the abdominal cavity obsolete_peritoneum true interpreting data Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data planning The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch planning Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting obsolete_documenting true histological sample preparation 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 PERSON:Bjoern Peters OBI branch derived histological sample preparation inductive reasoning Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer. a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns. BP: 10/22/122: After changing the parent class to drawing a conclusion *based on data* it is no longer clear that this class is needed; minimally it needs a better definition to distinguish it. Proposal is to obsolete. Bjoern Peters wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning inductive reasoning mass analyzer The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply. Frank Gibson PERSON: Daniel Schober http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer mass analyzer hypothesis-driven investigation is an investigation with the goal to test one or more hypothesis PlanAndPlannedProcess Branch OBI branch derived hypothesis-driven investigation hypothesis generating investigation is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis PlanAndPlannedProcess Branch OBI branch derived hypothesis generating investigation ion source The ion source of a Voyager-DE??? STR Biospectrometry Workstation An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))). Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source ion source ion detector The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q. Frank Gibson http://en.wikipedia.org/wiki/Mass_spectrometry#Detector ion detector Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019 An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism Philippe Rocca-Serra metabolite assay metabolomic assay OBI metabolite profiling assay light emission function A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. Bill Bug Daniel Schober Frank Gibson Melanie Courtot light emission function record function A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation Bill Bug Daniel Schober Frank Gibson Melanie Courtot record function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot magnify function contain function A syringe, a beaker A contain function is a function to constrain a material entities location in space Bill Bug Daniel Schober Frank Gibson Melanie Courtot contain function heat function A heat function is a function that increases the internal kinetic energy of a material Bill Bug Daniel Schober Frank Gibson Melanie Courtot heat function material separation function A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality. Bill Bug Daniel Schober Frank Gibson Melanie Courtot material separation function ionize process Electrospray ionization in mass spectrometry a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation. 2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize Person:Bjoern Peters ionize process excitation function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot excitation function freeze function A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material. Bill Bug Daniel Schober Frank Gibson Melanie Courtot freeze function synthesizing function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot synthesizing function perturb function A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function. Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Perturbation_biology perturb function filter function 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 mechanical function A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Mechanical_work mechanical 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 gas filter function liquid filter function A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture Frank Gibson liquid filter function transfer function A transfer function is a function to displace a material from one location to another. Bill Bug Daniel Schober Frank Gibson Melanie Courtot transfer function electricity supply function the function of supplying current during a neuroscience experiment. An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment. Daniel Schober Frank Gibson Melanie Courtot power supply electricity supply function ionization function The ion source in amass spectrometer 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot http://en.wikipedia.org/wiki/Ionization ionization function cool function A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material. Daniel Schober Frank Gibson Melanie Courtot cool function connection function An electricity cable 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot connection function isoelectric focusing device An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated. Frank Gibson isoelectric focusing unit sep:00097 isoelectric focusing device thermostatic circulator A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid Frank Gibson sep:00098 thermostatic circulator energy supply function An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy Frank Gibson energy supply function information processor function An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. Frank Gibson data processor function information processor function signal conversion function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot transduction function signal conversion function blot module A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised Frank Gibson sep:00092 blot module signal amplification function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot signal amplification function image acquisition function An image acquisition function is a function to acquire an image of a material Frank Gibson image acquisition function image acquisition device An image creation device is a device which captures a digitized image of an object Frank Gibson image acquisition device sep:00096 image creation device solid support function Taped, glued, pinned, dried or molecularly bonded to a solid support A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement Daniel Schober Frank Gibson Melanie Courtot solid support function display function A display function is a function to present information by translating that information through some lookup process into visual form. Bill Bug Daniel Schober Frank Gibson Melanie Courtot display function environment control function An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature. Bill Bug Daniel Schober Frank Gibson Melanie Courtot environment control function sort function A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order. Daniel Schober Frank Gibson Melanie Courtot sort function gel dryer A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels Frank Gibson sep:00094 gel dryer primer role a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation. (cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer primer role PCR product PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. is double stranded DNA that is the specified output of a polymerase chain reaction We are using PCR and not the written out words, as this is the most common used. GROUP: OBI BIomaterial Branch GROUP: OBI BIomaterial Branch PCR product viral RNA extraction The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703 The extraction of RNA from an input material that specifically isolates viral RNA Person:Bjoern Peters viral RNA extraction nucleic acid template role a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 a reference substance 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 recombinant plasmid a plasmid in which extraneous DNA has been inserted. PERSON: Bjoern Peters PERSON: Kevin Clancy PERSON: Melanie Courtot GROUP: OBI Biomaterial Branch recombinant plasmid cloning vector role pBluescript plays the role of a cloning vector A material to be added 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. JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/ PERSON: Helen Parkinson cloning vector role 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. a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle OBI PA Bjoern Peters and Nicole Washington cell cycle synchronization polymerase chain reaction Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 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. OBI Plan PCR adapted from wikipedai polymerase chain reaction cloning insert role 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. 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 Measuring glucose concentration in blood from a mouse. See Figure 2 of the 2016 OBI paper, PMID: 27128319. An assay that determines the concentration of glucose molecules in a blood serum sample Bjoern Peters OBI measuring glucose concentration in blood serum assay reverse transcriptase enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) person:Melanie Courtot group:OBI reverse transcriptase A trypsinized suspension of cells A material entity that has undergone a process of digestion with trypsin Person:Bjoern Peters obsolete_trypsinized material true 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 Philippe Rocca-Serra OBI Instrument adapted from Wikipedia syringe extract Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923 an extract is a material entity which results from an extraction process PERSON: Philippe Rocca-Serra extracted material GROUP: OBI Biomatrial Branch extract 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 An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity. This term should encompass transcription and post-transcription, but before translation into protein. So 'gene expression' itself is too broad, and we use 'transcription profiling identification objective' to constrain the scope of this term. Philippe Rocca-Serra gene expression profiling transcription profiling OBI transcription profiling assay averaging objective 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. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi averaging objective injection Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712 injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue. Philippe Rocca-Serra OBI Biomaterial injection enzyme (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more. person: Melanie Courtot GROUP:OBI enzyme intraperitoneal administration Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h The administration of a substance into the peritoneum of an organism Person:Bjoern Peters intraperitoneal administration plasmid plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 person:Melanie Courtot group:OBI plasmid injection into organ section Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology A process in which an input substance is injected into a organ section. Person:Bjoern Peters injection into organ section polyacrylamide gel Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143 a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution PERSON: Jie Zheng PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch polyacrylamide gel genotyping using an Affymetrix chip An assay with the objective to determine a sequence feature of DNA Bjoern Peters Philippe Rocca-Serra OBI DNA sequence feature detection assay adding material objective creating a mouse infected with LCM virus is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity BP adding material objective An assay 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. Philippe Rocca-Serra SNP analysis genotype profiling OBI Biomaterial genotyping assay needle 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 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. Philippe Rocca-Serra OBI Instrument needle analyte measurement objective The objective to measure the concentration of glucose in a blood sample an assay objective to determine the presence or concentration of an analyte in the evaluant PERSON: Bjoern Peters PPPB branch analyte measurement objective Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule. Philippe Rocca-Serra OBI Biomaterial DNA sequence variation detection assay 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 a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch agarose gel assay objective the objective to determine the weight of a mouse. an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role) PPPB branch PPPB branch assay objective Alan Ruttenberg's heart The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions Person:Bjoern Peters http://en.wikipedia.org/wiki/Heart obsolete_heart true example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant. Alan Ruttenberg Bjoern Peters Helen Parkinson Philippe Rocca-Serra Alan Ruttenberg Bjoern Peters Helen Parkinson OBI Planned process branch Philippe Rocca-Serra analyte assay target of material addition role peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. A role of a material entity that is realized in an "adding a material entity into a target" process where the bearer of the role (the target) receives the addition of another material entity. From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role. GROUP: Role Branch OBI target of material addition role The patients was weighed and mass was determined to be 47 kilograms An assay that determines the mass of an evaluant Helen Parkinson OBI mass measurement assay DNA cleavage assay for the identification of topoisomerase I inhibitors. Nat Protoc. 2008;3(11):1736-50. PMID: 18927559 a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval Philippe Rocca-Serra obsolete_identification true An electrophysiology assay where the recording location of the electrode is intracellular. Frank Gibson Frank Gibson intracellular electrophysiology recording assay packed column A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube. PERSON:Daniel Schober WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218 packed column example of subclass: normalized data set - A normalized data set is a data set that is produced as the output of a normalization data transformation. This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process. PERSON: Alan Ruttenberg PERSON: James Malone PERSON: Melanie Courtot obsolete_defined_output true regulatory agency The US Environmental Protection Agency A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. GROUP: OBI Biomaterial Branch WEB: en.wikipedia.org/wiki/Regulator regulatory agency normalized data set A data set that is produced as the output of a normalization data transformation. PERSON: James Malone PERSON: Melanie Courtot normalized data set measure function A glucometer measures blood glucose concentration, the glucometer has a 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: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson measure function The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron An electrophysiology assay where the recording location of the electrode is extracellular. Frank Gibson Helen Parkinson Frank Gibson extracellular electrophysiology recording assay consume data function 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. PERSON: Daniel Schober PERSON: Frank Gibson PERSON: Melanie Courtot consume data function material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective manufacturing A planned process with the objective 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 Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective column chromatography detector There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077 chromatography detector, defined class/xps column chromatography detector Bruker autosampler A Bruker autosampler is an autosampler made by Bruker. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209 Bruker autosampler 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099 organic acid column thermal conductivity detector The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity). PERSON:Daniel Schober TCD, hot wire detector WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084 thermal conductivity detector Bruker US 2 NMR magnet An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189 NMR instrument Bruker US 2 NMR magnet 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238 refactor as defined class protein column solvent mixer A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072 solvent mixer Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides. An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles. Philippe Rocca-Serra Philippe Rocca-Serra mass spectrometry assay study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that carries out 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. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. study design execution Bruker NMR Case sample changer The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203 NMR instrument Bruker NMR Case sample changer nano pump system A pump system optimized for nano flow chromatography. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052 nano pump system Bruker AutoClean system 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. washing system/NMR tube washing system, XPS: device has function washing PERSON:Daniel Schober WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205 Bruker AutoClean system manual injection system The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064 manual injection system Varian GEMINI spectrometer An older Varian Broadband NMR spectrometer. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239 NMR instrument Varian GEMINI spectrometer column connector A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236 chromatography device column connector solid NMR probe An NMR probe that is designed to hold a solid sample. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243 NMR device solid NMR probe Bruker high resolution probe 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. PERSON:Daniel Schober HR Probe GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223 NMR probe Bruker high resolution probe chromatography detector 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012 chromatography detector normal phase column A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097 normal phase column APOLLO console The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application. PERSON:Daniel Schober WEB:<http://www.tecmag.com/apollo.htm> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249 NMR instrument/NMR console APOLLO console NMR sample holder An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212 NMR device NMR sample holder chromatography instrument Any instrument that is used to carry out a chromatography experiment. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262 chromatography device, defined class? chromatography instrument continuous wave NMR instrument Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). PERSON:Daniel Schober WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283 NMR instrument continuous wave NMR instrument fourier transformation NMR instrument In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. PERSON:Daniel Schober GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284 NMR instrument fourier transformation NMR instrument nitrogen phosphorous detector 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 WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089 nitrogen phosphorous detector cation exchange column A cation exchange column is a chromatography column that is used in cation exchange chromatography. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096 cation exchange column direct detection NMR probe An NMR probe designed to allow the direct detection of acquisition nuclei. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280 NMR device direct detection NMR probe Bruker B-ACS system 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 WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210 NMR instrument Bruker B-ACS system rapid resolution column A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102 rapid resolution column liquid chromatography autosampler Designed to perform capillary LC with injection of sample volumes ranging from nL to L. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061 liquid chromatography autosampler vacuum degasser 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/topics/vacuum.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053 vacuum degasser capillary column A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066 capillary column sample inlet 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. PERSON:Daniel Schober WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044 chromatography device sample inlet NMR tube washing system An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204 NMR instrument NMR tube washing system NMR console A component of an NMR instrument that controls the activities of the other components. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015 NMR instrument, TODO: same as or part of acquisition computer? NMR console dual loop autosampler A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate). PERSON:Daniel Schober WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063 dual loop autosampler variable wavelength detector A chromatography detector, that can detect signals within a certain range at user-defined wavelengths. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079 variable wavelength detector Bruker LC-NMR platform The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276 NMR instrument hyphenated NMR instrument platform Bruker LC-NMR platform sample injection system An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057 chromatography device sample injection system multiple wavelength detector A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078 multiple wavelength detector photoionization detector 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. PERSON:Daniel Schober PID WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090 photoionization detector gas generator An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033 gas chromatography equipment gas generator column jacket A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276 chromatography device column jacket electron capture detector The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes. PERSON:Daniel Schober ECD WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085 electron capture detector 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106 reversed phase column injector lubricant A lubricant used in liquid chromatography that eases sample injector penetration. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118 injector lubricant isolation of cell population removing CD4+ cells from PBMCs using magnetic beads. a process in which a population of cells with certain characteristics is isolated from a larger population Person: Bjoern Peters isolation of cell population DISCOVERY console The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247 NMR instrument/NMR console DISCOVERY console Bruker AMX series NMR instrument 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. PERSON:Daniel Schober WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240 NMR instrument Bruker AMX series NMR instrument chromatofocusing column 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. PERSON:Daniel Schober WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209 chromatofocusing column 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.n 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 NMR instrument NMR probe NMR magnet A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185 NMR instrument NMR magnet trap column A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261 trap column flow probe An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes. PERSON:Daniel Schober WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131 NMR device flow probe Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters. An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a specimen collected from an organism in order to determine a phenotype of that organism. Philippe Rocca-Serra chemical pathology detection of analyte in blood sample url:https://en.wikipedia.org/wiki/Clinical_chemistry clinical chemistry assay flame ionization detector 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 FID WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197 flame ionization detector vial A container made from solid material and primarily used for holding liquid. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Vial vial magic angle spinning rotor 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. PERSON:Daniel Schober MAS rotor WEB:<http://www.freepatentsonline.com/4352066.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130 NMR instrument magic angle spinning rotor Varian VXR spectrometer A Varian NMR spectrometer. PERSON:Daniel Schober WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238 NMR instrument Varian VXR spectrometer splitless GC injector Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent. PERSON:Daniel Schober WEB:<http://en.wikipedia.org/wiki/Gas_chromatography> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060 splitless GC injector preparative autosampler For preparative LC with injection of sample volumes ranging from L to mL ranges. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062 preparative autosampler flow high resolution probe Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. PERSON:Daniel Schober flow HR-probe GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195 NMR probe flow high resolution probe liquid chromatography valve A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110 chromatography device liquid chromatography valve JEOL NMR probe An NMR probe that is manufactured by JEOL. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232 NMR device JEOL NMR probe Bruker UltraShield Plus NMR magnet An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190 NMR instrument Bruker UltraShield Plus NMR magnet 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:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191 NMR probe Bruker CryoProbe column cartridge A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055 column cartridge affinity column An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 affinity column tecmag NMR instrument An NMR instrument that is manufactured by tecmag. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250 NMR instrument tecmag NMR instrument gel filtration column A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 gel filtration column fraction collector 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. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/topics/fraction/collector.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073 fraction collector Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. PMID:18058796 An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping Philippe Rocca-Serra CNV analysis copy number variation profiling assay in-line filter 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 WEB:<http://www.appliedporous.com/frits-chromatography.htm> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123 in-line filter imaging NMR probe An NMR probe that is designed for generating pictures from sample states via NMR imaging. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244 NMR device imaging NMR probe isolation of adherent cells a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells. isolation of adherent cells Bruker AC series NMR instrument A series of older Bruker NMR magnets, now out of production. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241 NMR instrument Bruker AC series NMR instrument gas chromatography equipment Any device used in a gas chromatography experiment. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030 will become defined class/xps gas chromatography equipment syringe filter A small membrane filter of defined pore size, that filters samples from a syringe. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122 syringe filter Bruker SampleRail system This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207 NMR instrument Bruker SampleRail system column compartment 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068 column compartment capillary pump system A pump system optimized for capillary chromatography. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051 capillary pump system evaporative light scattering detector The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082 evaporative light scattering detector isolation of PBMCs cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs. a process in which cells with a single nucleus are isolated from a blood sample PERSON: bjoern peters wiki http://en.wikipedia.org/wiki/PBMC isolation of PBMCs column cartridger A chromatography device where the column cartridge is inserted into and stabilised. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054 column cartridger nitrogen generator A gas generator that generates nitrogen gas. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034 nitrogen generator needle assembly The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065 needle assembly reverse transcribed polymerase chain reaction Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group. Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW. Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094 reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity. 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation Philippe Rocca-Serra RT-PCR reverse transcription polymerase chain reaction reverse transcribed polymerase chain reaction Bruker Capillary LC-NMR platform Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279 NMR instrument hyphenated NMR instrument platform Bruker Capillary LC-NMR platform gas chromatography oven A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039 gas chromatography equipment gas chromatography oven autosampler An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002 NMR instrument autosampler isocratic pump system A pump system optimized for isocratic chromatography. PERSON:Daniel Schober WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049 isocratic pump system flash pump system Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048 flash pump system Varian UNITY INOVA spectrometer The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips. PERSON:Daniel Schober WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236 NMR instrument Varian UNITY INOVA spectrometer liquid NMR probe An NMR probe that is designed to hold a liquid sample. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242 NMR device liquid NMR probe ion exchange column An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105 ion exchange column Bruker NMR probe An NMR probe that is manufactured by Bruker. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231 NMR device, TODO: May need no definition. Bruker NMR probe anion trap column An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277 anion trap column fluorescene detector 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 WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080 fluorescene detector 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248 NMR probe tecmag EAGLE probe electrical conductivity detector 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 WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239 electrical conductivity detector NMR instrument An Instrument which is used to carry out a NMR analysis of some sample. PERSON:Daniel Schober MRI scanner NMR instrument magnetic resonance imaging scanner GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059 NMR instrument NMR instrument Bruker UltraShield NMR magnet 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. PERSON:Daniel Schober 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 NMR instrument Bruker UltraShield NMR magnet piston-seal The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116 piston-seal mass selective detector A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier. PERSON:Daniel Schober mass spectrometry detector WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198 mass selective detector spin column 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232 spin column manufacturer role 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 is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role transfer line A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system. PERSON:Daniel Schober WEB:<http://www.freepatentsonline.com/5702671.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235 chromatography device transfer line gradient pump system A pump system optimized for gradient chromatography. PERSON:Daniel Schober WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050 gradient pump system high temperature column A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233 high temperature column Bruker Ultrastabilized NMR magnet 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. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188 NMR instrument Bruker Ultrastabilized NMR magnet scattered molecular aggregate the sodium and chloride ions in a glass of salt water 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 PERSON: Alan Ruttenberg Collective 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 scattered molecular aggregate the phosphate concentration should be 0.1M A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity. PERSON: Alan Ruttenberg Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. obsolete_molecular concentration true NMR sample tube 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 GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132 NMR device NMR sample tube Varian UNITY spectrometer The predecessor series of the Varian UNITY INOVA spectrometer. PERSON:Daniel Schober WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237 NMR instrument Varian UNITY spectrometer AVANCE II spectrometer A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently. PERSON:Daniel Schober WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197 NMR instrument AVANCE II spectrometer 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237 y-column connector Bruker LC-NMR/MS platform Includes the connection to a high-resolution TOF-LC-MS system. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277 NMR instrument hyphenated NMR instrument platform Bruker LC-NMR/MS platform refractive index detector For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081 refractive index detector anion exchange column An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095 anion exchange column plunger column 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108 plunger column flame photometric detector 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. PERSON:Daniel Schober FPD WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091 flame photometric detector chromatography pump system Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography). PERSON:Daniel Schober WEB:<http://en.wikipedia.org/wiki/Column_chromatography> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046 chromatography pump system Bruker 1mm MicroProbe Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling available. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194 NMR probe Bruker 1mm MicroProbe 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. PERSON:Daniel Schober Bruker Efficient Sample Transfer NMR WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206 NMR instrument Bruker BEST NMR system chromatography detector filter 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 cation trap column A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278 cation trap column column adapter An Adapter that enabled the connection of a column to additional devices. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113 chromatography device column adapter pulsed amperometric detector A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC). PERSON:Daniel Schober PAD WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240 pulsed amperometric detector Bruker NMR instrument An NMR instrument that is manufactured by Bruker. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198 NMR instrument Bruker NMR instrument Bruker NMR magnet An NMR magnet that is manufactured by Bruker. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186 NMR instrument Bruker NMR magnet ozone-induced chemiluminescence detector 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. PERSON:Daniel Schober WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088 ozone-induced chemiluminescence detector tecmag NMR console An NMR console manufactured by tecmac. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246 NMR instrument tecmag NMR console JEOL NMR instrument An NMR instrument that is manufactured by JEOL. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226 NMR instrument JEOL NMR instrument chromatography consumable A chromatography consumable is a consumable that is used in a chromatography experiment. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115 chromatography device chromatography consumable column frit A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density). PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/topics/radial/columns.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070 chromatography device column frit liquid chromatography column A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227 liquid chromatography column detector lamp A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119 detector lamp chart recorder 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. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069 chromatography device chart recorder 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 WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219 open tubular column high resolution magic angle spin probe 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. PERSON:Daniel Schober high resolution MAS, hr-MAS GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192 NMR probe high resolution magic angle spin probe hydrogen generator A gas generator that generates hydrogen gas. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035 hydrogen generator glass column 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 GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101 glass column auto injector A gas chromatography device that can auto-inject a small number of samples an inlet. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058 auto injector Varian NMR instrument 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 NMR instrument Varian NMR instrument Bruker MATCH tube holder system 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.n 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. PERSON:Daniel Schober Bruker Multiple Adjustable Tube Clamp Holder GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211 NMR instrument Bruker MATCH tube holder system Bruker SPE-NMR platform A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278 NMR instrument hyphenated NMR instrument platform Bruker SPE-NMR platform guard column Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111 chromatography device guard column Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach. PMID:19077203 An assay that determines protein expression and translation activity using protein extracts collected from a material entity. Phlippe Rocca-Serra proteomic analysis OBI branch derived protein expression profiling assay high resolution probe with automatic tuning and matching 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. PERSON:Daniel Schober High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224 NMR probe high resolution probe with automatic tuning and matching fluorine-induced chemiluminescence detector A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator. PERSON:Daniel Schober WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087 fluorine-induced chemiluminescence detector size exclusion column A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100 size exclusion column chromatography splitter An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041 chromatography device chromatography splitter Bruker micro imaging probe 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. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/probes_microimaging.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225 NMR probe Bruker micro imaging probe custom made column A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234 custom made column gel permeation column A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size. PERSON:Daniel Schober WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103 gel permeation column Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202 An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures. Philippe Rocca-Serra Nuclear magnetic resonance spectroscopy url:https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy NMR spectroscopy assay Bruker SampleJet system Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/automation.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208 NMR instrument Bruker SampleJet system JEOL ECX NMR spectrometer 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 NMR instrument JEOL ECX NMR spectrometer Illumina (Solexa) sequencing is an example of DNA sequencing A sequencing assay which determines information on the sequence of a DNA molecule. Philippe Rocca-Serra nucleotide sequencing url:https://en.wikipedia.org/wiki/DNA_sequencing DNA sequencing assay quaternary pump system A pump system that pump and mix up to four different solvents in parallel. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047 quaternary pump system carbon nanotube column 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. PERSON:Daniel Schober WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107 carbon nanotube column Bruker solid magic angle spinning probe Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. PERSON:Daniel Schober solid MAS probe GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193 NMR probe Bruker solid magic angle spinning probe Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology._PMID:18702943 An assay that studies phenotypes of an organism involving its blood and blood producing organs using a variety of techniques and instruments Philippe Rocca-Serra blood analysis haematology OBI branch derived hematology assay Varian MERCURY spectrometer MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation. PERSON:Daniel Schober WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235 NMR instrument Varian MERCURY spectrometer Bruker Metabolic Profiler 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. PERSON:Daniel Schober WEB:<http://www.bruker-biospin.com/metabolicprofiler.html> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199 NMR instrument hyphenated NMR instrument platform Bruker Metabolic Profiler column heater The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure. PERSON:Daniel Schober WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040 column heater 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._PMID:18218979 An assay that measures the 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. Philippe Rocca-Serra DNA methylation profiling OBI branch derived DNA methylation profiling assay JEOL CapNMR probe The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility. PERSON:Daniel Schober WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233 NMR probe JEOL CapNMR probe acquisition computer A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013 NMR instrument acquisition computer 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. PERSON:Daniel Schober FID WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083 chromatography detector, defined class/xps gas chromatography detector gas purifier Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems. PERSON:Daniel Schober WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036 gas chromatography equipment gas purifier material separation objective The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. PPPB branch PPPB branch material separation objective indirect detection probe An NMR probe designed to allow the indirect detection of acquisition nuclei. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281 NMR device indirect detection probe JEOL ECA NMR spectrometer The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world. PERSON:Daniel Schober WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx> http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228 NMR instrument JEOL ECA NMR spectrometer 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. PERSON:Daniel Schober AED WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086 atomic emission detector clustered data set A clustered data set is the output of a K means clustering data transformation 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. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels AR thinks could be a data item instead clustered data set data set of features 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. PERSON: James Malone PERSON: Monnie McGee data set of features differential expression analysis data transformation A differential expression analysis data transformation is a data transformation that has an objective of differential expression analysis. Frequently this data transformation involves summarizing or otherwise aggregating signals from various samples categorized into groups, and calculating measures of group differences from these aggregated signals. Dan Berrios James Malone Melanie Courtot Monnie McGee WEB: differential expression analysis data transformation urine specimen a portion of urine collected from an organism 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. 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 are we happy calling collection of urine a material separation? urine specimen 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. created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. bp bp material combination fuzzy clustering objective A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori. James Malone PERSON: James Malone PERSON: Ryan Brinkman fuzzy clustering objective device setting 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 a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133 PERSON: Frank Gibson device setting blood specimen blood drawn from a human for glucose assay a material entity derived from a portion of blood collected from an organism Bjoern Peters Bjoern Peters blood specimen data set of predicted values according to fitted curve 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. PERSON: James Malone PERSON: Monnie McGee data set of predicted values according to fitted curve data representational model The Cytoscape application is commonly used to visualize data representational models about biological entities. It can read and write several serializations of data representational models, including BioPAX. gene regulatory graph model phylogenetic tree protein interaction network An information content entity representing the relationships between data items. Melanie Courtot data structure data structure specification GROUP: OBI 2009-02-28: work on this term has been finalized during the OBI workshop winter 2009 data representational model drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation, collecting a stone from a site A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed. Definition updated following discussion on 2024-10-07 OBI dev call. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process background corrected data set A data set that is produced as the output of a background correction data transformation. PERSON: James Malone PERSON: Melanie Courtot background corrected data set 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. An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte. IEDB ELISA IEDB enzyme-linked immunosorbent assay error corrected data set 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). PERSON: James Malone PERSON: Monnie McGee error corrected data set class prediction data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. James Malone supervised classification data transformation PERSON: James Malone class prediction data transformation 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 cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies. IEDB IEDB BrdU incorporation assay Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. IEDB ICCS ICS IEDB intracellular cytokine staining (ICS) obsolete intracellular cytokine staining assay true background correction data transformation A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction. James Malone PERSON: James Malone background correction data transformation Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes. An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer IEDB MHC tetramer assay IEDB MHC tetramer/multimer staining obsolete MHC multimer staining assay true error correction data transformation An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation. James Malone Monnie McGee EDITORS error correction data transformation 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 tritiated thymidine, and using a scintillation counter to detect the radioactivity. A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. IEDB IEDB tritiated thymidine incorporation assay sample from organism a material obtained from an organism in order to be a representative of the whole 5/29: This is a helper class for now we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about. sample from organism statistical hypothesis test A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. James Malone PERSON: James Malone statistical hypothesis test center value A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. PERSON: James Malone PERSON: Monnie McGee median center value statistical hypothesis test objective is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation. James Malone Person:Helen Parkinson hypothesis test objective WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing statistical hypothesis test objective reduced dimension data set 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. PERSON: James Malone PERSON: Monnie McGee reduced dimension data set portioning objective The objective to obtain multiple aliquots of an enzyme preparation. A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material. portioning objective average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean average value whole organism preparation putting a mouse in the blender. Not: putting a mouse on a scale 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 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. whole organism preparation separation into different composition objective The objective to obtain cells contained in a sample of blood. A material separation objective aiming 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). We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives separation into different composition objective Study result is an information content entity that is a specified data output of a study. GROUP: OBI obsolete_study result true The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification that is fulfilled by obtaining a material entity for potential use as an input upon which measurements or observations are performed. OBI recommends against subclassing this term in order to avoid further parallel hierarchies between this term and specimen collection process. Bjoern Peters Bjoern Peters specimen collection objective creating a mixture of molecules in solution The production of PBS is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. Bjoern Peters PERSON: Helen Parkinson creating a mixture of molecules in solution material combination objective is an objective to obtain an output material that contains several input materials. PPPB branch bp material combination objective nucleotide overhang cloning 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 Helen Parkinson nucleotide overhang cloning rodent care protocol Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. A rodent care protocol is an animal protocol in which the animals being taken care of are rodents. Bjoern Peters Bjoern Peters rodent care protocol 454 Genome Sequence 20 PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults. Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20. is a DNA sequencer first manufactured by 454 Life Science Corporation in 2005, and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. Philippe Rocca-Serra GS 20 454 Genome Sequence 20 immunoprecipitation PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity Philippe Rocca-Serra OBI plan and planned process branch immunoprecipitation ABI 377 automated sequencer 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. Philippe Rocca-Serra Applied Biosystems ABI 377 automated sequencer recombination enzyme based cloning a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector recombination enzyme based cloning PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gr�_f S, Johnson N, Herrero J, Tomazou EM, Thorne NP, B�_ckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavar�� S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85. A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods. Philippe Rocca-Serra Methylated DNA immunoprecipitation sequencing assay url:https://en.wikipedia.org/wiki/Methylated_DNA_immunoprecipitation MeDIP-seq assay animal feeding giving crickets to a snake. animal feeding is a process in which animals are provided with food In an investigation, this will typically be part of an animal care process Bjoern Peters branch derived animal feeding PMID: 271968. DNA sequencing with chain-terminating inhibitors. A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position Philippe Rocca-Serra Sanger sequencing dye terminator sequencing url:https://en.wikipedia.org/wiki/Sanger_sequencing chain termination sequencing assay 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. is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation Philippe Rocca-Serra Applied Biosystems AB SOLiD System PMID: 18388294. Single-molecule DNA sequencing of a viral genome. A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length. Philippe Rocca-Serra true single molecule sequencing url:https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing Helicos sequencing assay A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule Kevin Clancy, Bjoern Peters ligase obsolete_DNA ligase true An assay that measures the occurrence of death events in one or more organisms over time survival assessment assay 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. James Malone Ryan Brinkman SVM PERSON: Ryan Brinkman support vector machine self-organizing map A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these. James Malone Ryan Brinkman SOM PERSON: Ryan Brinkman self-organizing map 454 Genome Sequencer FLX PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B. J Biotechnol. 2008 Aug 31;136(1-2):3-10. is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. Philippe Rocca-Serra 454 GS FLX GS-FLX adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay 454 Genome Sequencer FLX Illumina Genome Analyzer II PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology Philippe Rocca-Serra Illumina Corporation Illumina Genome Analyzer II decision tree induction objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. James Malone decision tree induction objective Determination of the amino acid sequence of a peptide eluted from HLA-DRB1*04:01 to be VYPEVTVYPAKT. A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis. IEDB IEDB Edman degradation PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108. A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles. Philippe Rocca-Serra url:https://en.wikipedia.org/wiki/ABI_Solid_Sequencing SOLiD sequencing assay decision tree building data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. James Malone PERSON: James Malone decision tree building data transformation laboratory animal care a process that realizes an animal care protocol that specifies how animals are kept and maintained laboratory animal care yeast artificial chromosome vector a double-stranded DNA 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 this should be a child of 'chromosome' if we import that from another source Kevin Clancy, Bjoern Peters YAC yeast artificial chromosome vector Li-Cor 4300 DNA Analysis System is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing Philippe Rocca-Serra OBI and Li-Cor Li-Cor 4300 DNA Analysis System library preparation 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. 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. Philippe Rocca-Serra library construction library preparation pathogen challenge The administration of a live pathogenic organism to a host. pathogen challenge GenePattern software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ GenePattern software graph of vertices For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix. Bjoern Peters Chris Stoeckert James Malone WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html graph of vertices animal care protocol Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily. An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes Bjoern Peters Bjoern Peters animal care protocol PMID: 19275939 An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin Bjoern Peters Philippe Rocca-Serra chromatin immunoprecipitation sequencing assay url:https://en.wikipedia.org/wiki/ChIP-sequencing ChIP-seq assay HeliScope Single Molecule Sequencer is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry Philippe Rocca-Serra HeliScope Single Molecule Sequencer pathogen role Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383 pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role GROUP: Role Branch OBI 6 April 2009: from the Vaccine Community pathogen role vaccine preparation The production of B. pertussis vaccine. A planned process with the objective to create a vaccine. OBI vaccine production immunologic adjuvant role 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 The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen. 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'. GROUP: Role branch Vaccine Ontology, Wikipedia, OBI Renamed from adjuvent role, to be a more specific useage for immunology, tracker https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2887909&group_id=177891 immunologic adjuvant role PMID: 19527607 An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance. Philippe Rocca-Serra NuGO OBI plan branch glucose tolerance test paired-end library 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. is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs Philippe Rocca-Serra mate-paired library paired-end tag (PET) library adapted from information provided by Solid web site paired-end library ABI Solid Sequencing uses the ligation-based DNA sequencing technology (https://en.wikipedia.org/wiki/ABI_Solid_Sequencing). A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase Philippe Rocca-Serra url:https://en.wikipedia.org/wiki/Sequencing_by_ligation DNA sequencing by ligation assay PMID: 18987734 A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing. Philippe Rocca-Serra reversible terminator sequencing Solexa web site (SS_DNAsequencing.pdf document available on july 2009) Solexa sequencing assay host role In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09 host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role 30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition GROUP: Role Branch 30 Mar09 submitted by vaccine community OBI http://en.wikipedia.org/wiki/Host_(biology) host role 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 James Malone Ryan Brinkman PERSON: Ryan Brinkman peak matching k-nearest neighbors A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. James Malone k-NN PERSON: James Malone k-nearest neighbors rodent care keeping animal rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research. PPPB branch PPPB branch rodent care 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. Note: 'cloning vector role' is really a function. Should be dealt with globally cloning plasmid Pyrosequencing sheds light on DNA sequencing. PMID:1115661 A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin. Philippe Rocca-Serra url:http://en.wikipedia.org/wiki/Pyrosequencing pyrosequencing assay recombinant vector 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 restriction enzyme The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG an enzyme that has a specific target cleavage sites within nucleic acids Kevin Clancy, Bjoern Peters 5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments restriction enzyme Roche-454 pyrosequencing and Illumina (Solexa) sequencing use synthesis-based method for DNA sequencing A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step. Philippe Rocca-Serra url:https://www.illumina.com/technology/next-generation-sequencing/sequencing-technology.html DNA sequencing by synthesis assay NTP-2000 a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents Jennifer Fostel, Bjoern Peters NTP-2000 single fragment library is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs Philippe Rocca-Serra fragment library single fragment library 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. cloning vector restriction enzyme based cloning 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. Kevin Clancy, Bjoern Peters restriction enzyme based cloning 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 WEB: http://en.wikipedia.org/wiki/T-test Student's t-test material sample role a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general. 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 topologically preserved clustered data set the output data set generated from a self-organizing map. A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived. James Malone PERSON: James Malone topologically preserved clustered data set nucleic acid restriction enzyme digest A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site Kevin Clancy, Bjoern Peters nucleic acid restriction enzyme digest Measuring if a Hepacivirus C (HCV) infected patient has an antibody response to HCV core protein by ELISA. An assay that determines information about an immune response Bjoern Peters Randi Vita IEDB immune response assay material sampling process A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity sample collection sampling https://github.com/obi-ontology/obi/issues/1002 material sampling process material sample blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role OBI: workshop sample sample population https://github.com/obi-ontology/obi/issues/1013 material sample PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J. A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location. Philippe Rocca-Serra Sagar Jain url:https://en.wikipedia.org/wiki/Bisulfite_sequencing bisulfite sequencing assay CART A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone classification and regression trees BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. CART independent variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable. 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 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. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert experimental factor independent variable Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study factor study design independent variable dependent variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable. 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. 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. In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert dependent variable WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study design dependent variable anticoagulant-containing test tube A 'blue top' test tube that contains anticoagulant for storing blood specimens' Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case anticoagulant-containing test tube controlled variable specification In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, age is a controlled variable. Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent. 2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid In the Philly 2013 workshop the label was chosen to distinguish it from "controlled variable" as used in statistical modelling PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert controlled variable WEB: http://en.wikipedia.org/wiki/Control_variable 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI. study design controlled variable PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit. An assay that measures the amount of antithrombin III in blood. Alan Ruttenberg AT-III assay url:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06 human antithrombin-III in blood assay 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 fluorescently labeled MHC multimer survival rate A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring. Oliver He adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate survival rate recombinant BAC cloning 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 http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome recombinant BAC cloning multiple testing correction objective Application of the Bonferroni correction 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 multiple testing correction objective statistical model validation 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 A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation double blind study execution A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#double 2009/09/28 Alan Ruttenberg. Fucoidan-use-case double blind study execution SO:0000235 PLace_holder for sequence ontology term https://github.com/obi-ontology/obi/issues/1553 obsolete transcription factor binding site true glucometer Diabetic patients use glucometers to determine their glucose levels A measurement device with the function to measure and record the level/amount of glucose in a blood sample PERSON:Frank Gibson PERSON:Helen Parkinson glucose meter http://en.wikipedia.org/wiki/Glucose_meter glucometer purification objective the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. 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 BP 10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality purification objective SIINFEKL' is the primary structure of a peptide The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters obsolete_primary structure of protein true capsule shell a small rounded gelatinous container Person:Alan Ruttenberg http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n 2009/09/28 Alan Ruttenberg. Fucoidan-use-case capsule shell recombinant phage cloning Insert selection by BamHI methyltransferase protection in P1 phage-based 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 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 recombinant phage cloning cross linking cross linking can be used as a probe to link proteins together, to check protein protein interactions A process in which bonds are created that link one polymer to another PERSON: Chris Stoeckert http://en.wikipedia.org/wiki/Cross-link cross linking spike train datum Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. needs more work to see exactly what the data set looks like - HP Helen Parkinson, Alan Ruttenberg spike train measurement Jessica Turner, NIF spike train datum PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA). An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample. Alan Ruttenberg url:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06 prothrombin time assay denaturing Denaturing DNA in alcohol Is a process in which the tertiary or secondary structure of a polymer is disrupted http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 denaturing informing investigator of subject study arm Informing the investigator whether a patient is receiving a placebo or a treatment with an investigational compound. A planned process with the objective to make the investigator aware of which study arm a patient is participating in. 09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case informing investigator of subject study arm 1 An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard AT-III assay url:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 antithrombin-III berichrome assay material maintenance objective An objective specification maintains some or all of the qualities of a material over time. PERSON: Bjoern Peters PERSON: Bjoern Peters material maintenance objective presentation of stimulus The presentation of a flashing light to a monkey during reward training A planned process with the objective to expose an organism to a stimulus. Helen Parkinson, Jessica Turner, Dirk Derom stimulation of organism Helen Parkinson, Jessica Turner, Dirk Derom presentation of stimulus PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland). An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where 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. Alan Ruttenberg url:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06 spectrolyse heparin antifactor-Xa assay amplified DNA Amplied DNA created by PCR DNA that has been produced in an enzymatic amplification process PERSON: Alan Ruttenberg Alan Ruttenberg amplified DNA informed consent process A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate. 09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity. Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#informed 2009/09/28 Alan Ruttenberg. Fucoidan-use-case informed consent process a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues placeholder for SO BP et al obsolete primary structure of DNA macromolecule true 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 An assay that measures neural activity in the caudate nucleus Helen Parkinson Dirk Derom, OBI Jessica Turner, NIF measuring neural activity in the caudate nucleus assay to be treated with active ingredient role Role of a patient in a group treated with an active substance in a clinical trial 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 Person:Alan Ruttenberg PERSON: Helen Parkinson 2009/09/28 Alan Ruttenberg. Fucoidan-use-case to be treated with active ingredient role guar gum Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder. Helen Parkinson http://en.wikipedia.org/wiki/Guar_gum guar gum 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 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Berichrom(r) Antithrombin III (A) Kit micro electrode A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system. Helen Parkinson, Jessica Turner, Dirk Derom micro electrode measuring device Jessica Turner, Dirk Derom micro electrode fucoidan Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber). Helen Parkinson http://en.wikipedia.org/wiki/Fucoidan fucoidan calibration the process of using pH buffer adjust a pH meter A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements. GROUP: OBI Philly workshop WEB:http://en.wikipedia.org/wiki/calibration calibration anticoagulant tube storage of blood specimen Storage of a blood specimen in a tube with anticoagulant Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case anticoagulant tube storage of blood specimen The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent (PMID:19696660) An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy. There is also the 'partial thromboplastin assay', which some people use synonymously to aPPT, but historically was done slightly differently (without adding a coagulant). Alan Ruttenberg OBI call aPTT assay url:http://www.ebi.ac.uk/ols/ontologies/efo/terms?short_form=EFO_0004310 activated partial thromboplastin time assay filled capsule A pill in the form of a small rounded gelatinous container with medicine inside. Person:Alan Ruttenberg http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n 2009/09/28 Alan Ruttenberg. Fucoidan-use-case filled capsule single blind study execution A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated Person:Alan Ruttenberg http://clinicaltrials.gov/ct2/info/glossary#single 2009/09/28 Alan Ruttenberg. Fucoidan-use-case single blind study execution PMID:19696660#The thrombin time was determined using thromboclotin assay kit. An assay that measures the time between the addition of the thrombin and the clot formation in plasma. Alan Ruttenberg url:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06 thrombin time assay recombinant YAC cloning Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21 Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material Helen Parkinson http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611 recombinant YAC cloning to be treated with placebo role 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 Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case to be treated with placebo role treatment portion of study execution A planned process, part of a study design execution, during which the treatment of subjects is ongoing 09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case treatment portion of study execution pill A dose of medicine or placebo in the form of a small pellet. Person:Alan Ruttenberg http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n 2009/09/28 Alan Ruttenberg. Fucoidan-use-case pill research organization The SALK institute is a research organization. An organization formed with a goal to have its members conduct investigations Person:Bjoern Peters research organization A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds Person:Bjoern Peters obsolete_primary structure of sequence macromolecule true DNA residue methylation a quality of a DNA residue that has a methyl group attached to it DNA residue methylation measurement device A ruler, a microarray scanner, a Geiger counter. A device in which a measure function inheres. GROUP:OBI Philly workshop OBI measurement device high molecular weight DNA extract Extraction of chromosomal DNA from mammalian cells by first isolating nucei The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas. PERSON:Chris Stoeckert OBI high molecular weight DNA extract manufacturer A person or organization that has a manufacturer role. manufacturer test tube A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material Bjoern Peters collection tube sample tube http://en.wikipedia.org/wiki/Test_tube test tube oral ingestion of pill An adding a material entity to target with the entity is a pill and the target is the mouth Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case oral ingestion of pill material maintenance A planned process with the objective to maintain some or all of the characteristics of an input material over time. material maintenance labeled oligonucleotide a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide 2010-01-31: Philippe Rocca-Serra placeholder Person: Philippe Rocca-Serra labeled oligonucleotide unblinding process A planned process that is the part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials. Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case unblinding process subject agrees they understand informed consent document A planned process in which a subject receives an informed consent document and agrees that they have understood it. 09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case subject agrees they understand informed consent document informing subject of study arm Informing participants whether they are receiving a placebo or a treatment with an investigational compound. A planned process with the objective to make the subject aware of which study arm they are participating in. 09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort Person:Alan Ruttenberg 2009/09/28 Alan Ruttenberg. Fucoidan-use-case informing subject of study arm Sysmex CA-6000 Coagulation Analyzer The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays Person:Alan Ruttenberg web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Sysmex CA-6000 Coagulation Analyzer 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] A medical organization at which sick or injured people are given clinical care Person:Alan Ruttenberg Person:Helen Parkinson modified from the wording of the wordnet definition; http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n https://github.com/obi-ontology/obi/issues/1295 obsolete hospital true The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together Person:Bjoern Peters obsolete primary structure of RNA molecule true test substance role 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 Person:Alan Ruttenberg Group:OBI test substance role polyA RNA extraction A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. Person: Chris Stoeckert Person: Jie Zheng UPenn Group polyA RNA extraction organellar RNA extraction A RNA extraction process in which the desired output material is RNA in the organelle(s). Person: Chris Stoeckert Person: Jie Zheng UPenn Group organellar RNA extraction obsolete_diethyl pyrocarbonate true record of missing knowledge A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. An information content entity created to indicate that information about something is not available to the person recording it. This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. Bjoern Peters record of missing knowledge Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest. An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. IEDB Philippe Rocca-Serra IEDB Philippe Rocca-Serra western blot assay total RNA extraction A RNA extraction process in which total cellular and organelle RNA are extracted. Person: Chris Stoeckert Person: Jie Zheng UPenn Group total RNA extraction An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer. intracellular staining obsolete intracellular material detection by flow cytometry assay true complementary nucleotide probe role A primer in a PCR reaction. A probe on an Affymetrix chip. A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence PERSON:Bjoern Peters complementary nucleotide probe role record of unknown sex A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record. a record indicating that the biological sex of an organism is not known. I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement. Bjoern Peters record of unknown sex cytoplasmic RNA extraction A RNA extraction process in which the desired output material is RNA in the cytoplasm. Person: Chris Stoeckert Person: Jie Zheng UPenn Group cytoplasmic RNA extraction The level of actin mRNA levels in normal and diseased tiisue was measured using a northern blot assay. An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager. Philippe Rocca-Serra Richard Scheuermann northern blot northern blot assay Likelihood-ratio test Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models. Tina Boussard Likelihood-ratio test nuclear RNA extract Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30) A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group nuclear RNA extract A serum neutralization of viral infectivity assay which is performed in a 96-well plate. Bjoern Peters Melanie Courtot microneutralization assay 96-well neutralization assay establishing cancer cell line Establishment of HeLa immortal cell line is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal Helen Parkinson establishing cancer cell line pattern matching objective A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees. Tina Boussard http://en.wikipedia.org/wiki/Pattern_matching pattern matching objective polyA RNA extract Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.) A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group polyA RNA extract An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. Philippe Rocca-Serra RNAO single-nucleotide-resolution nucleic acid structure mapping assay Determining the viral titer of a virus infected human by measuring the presence of hemagglutination when dilutions of serum samples are added to a known quantity of red blood cells. An assay that quantifies viruses by their hemagglutination activity. Bjoern Peters Melanie Courtot Randi Vita HA HI viral haemagglutinin assay url:http://en.wikipedia.org/wiki/Hemagglutination_assay viral hemagglutination assay An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked. Bjoern Peters Melanie Courtot influenza neutralization assay url:http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/ serum neutralization of viral infectivity assay pre-mortem specimen material obtained through a liver biopsy from a human patient a specimen that was taken from a live organism Bjoern Peters MO_705 premortem pre-mortem specimen Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays. An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. IEDB IEDB detection of specific nucleic acid polymers with complementary probes Examining the ability of a monoclonal antibody to inhibit hemagglutination by Influenza A virus by comparing the levels of hemagglutination with and without the presence of the antibody. An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors. Bjoern Peters Melanie Courtot Randi Vita HAI HIA biological activity hemagglutination inhibition viral haemagglutinin inhibition assay OBI branch derived viral hemagglutination inhibition assay cytoplasmic RNA extract Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. PERSON:Chris Stoeckert UPenn Group cytoplasmic RNA extract cell line immortalization Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line 4-20-13 MHB: This class was repositioned as a child of 'establishing cell line', based on the existing definition ("the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro"), and examples and other annotations indicating the intent to describe a process through which a new immortal cell line is established from an existing mortal cell line using genetic modification techniques. The definition above was modified to clarify this perspective. Bjoern Peters 'establishing immortal cell line through directed genetic modification' OBI A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line. cell line immortalization random primed DNA labeling PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9. a labeling in which random primers are used to uniformly label input DNA need to add Klenow subunit of DNA polymerase I under material entity Person: Bjoern Peters Person: Chris Stoeckert Person: Philippe Rocca-Serra PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13. random primed DNA labeling RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng Group: UPenn Group RNA extract Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. A cytometry assay that monitors a cell population to track how many are killed by other cells. IEDB IEDB cell-cell killing assay Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells. A cell killing assay that measures if and how many target cells are killed within an organism. IEDB IEDB in vivo cell killing assay secondary structure of sequence macromolecule A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford. 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO Person: Philippe Rocca-Serra Wikipedia secondary structure of sequence macromolecule nuclear RNA extraction A RNA extraction process in which the desired output material is RNA in the nucleus. Person: Chris Stoeckert Person: Jie Zheng UPenn Group nuclear RNA extraction survival curve A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://www.graphpad.com/www/book/survive.htm survival curve Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation. A cytometry assay which measures the degreee to which input cells are replicating. IEDB IEDB cell proliferation assay PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity. Marcus Chibucos Philippe Rocca-Serra Southern blot OBI Southern blot assay An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. Bjoern Peters Melanie Courtot Q-PCR kinetic polymerase chain reaction qPCR quantitative real time polymerase chain reaction url:http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real time polymerase chain reaction assay protein extract PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE. J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23. a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation, Person: Philippe Rocca-Serra OBI & wikipedia protein extract total RNA extract Extraction of total RNA from cells with Qiagen mini RNeasy kit A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group total RNA extract secondary structure of RNA molecule PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA. 2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO Person: Philippe Rocca-Serra secondary structure of RNA molecule PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28. A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe Philippe Rocca-Serra RNA ontology DEPC structure mapping assay organellar RNA extract Extraction of organellar RNA from plant cells using organellar RNA binding protein. A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group organellar RNA extract post mortem specimen the spleen taken from a dead mouse a specimen that was taken from a dead organism Bjoern Peters MO_416 postmortem post mortem specimen Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100. A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture. IEDB IEDB in vitro cell killing assay CTLL-2 cells were grown in the presence of hybridoma supernatants and their growth was monitored by a 3H-thymidine incorporation cell proliferation assay in order to detect IL-2 in the hybridoma supernatant. An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant. IEDB IEDB reporter cell line analyte detection bioassay sequence feature annotation Information about a sequence region Bjoern Peters Bjoern Peters place holder for sequence ontology term sequence feature annotation induced hemagglutination The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances MC, 20100217: This term was originally submitted to GO, see discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=2947975&group_id=36855&atid=440764. After discussion it was agreed that this isn't a natural in vivo process and therefore out of scope for GO. Dev call Nov 22, 2010: To reflect this, the term's label has been updated to 'induced hemagglutination'. person: Bjoern Peters person: Melanie Courtot hemeagglutination WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination induced hemagglutination supplying Jackson Labs supplies mouse strains. A planned process with the objective to provide material entities to be used in an investigation. Jennifer Fostel Jennifer Fostel 5/31/2012: A supplying process implies that there is an acquisition process. These may need to be tied together, so that modeling either way is reciprocal. supplying labeled DNA extract a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call Group: OBI group Group: OBI group labeled DNA extract cell specimen type of sample used in the PCIRN influenza network A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf cloacal specimen To evaluate the specificity of antibody binding to 35S-labeled IA-2(256-760) in comparison with 35S-labeled IA-2IC construct, the mutual inhibition activity of different concentrations of unlabeled IA-2IC and/or IA-2(256-760) fragments were tested. Unlabeled recombinant IA-2(256-760) and/or IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were added to each tube and incubated overnight at 4C with patient sera. The following day, after incubation with radiolabeled 35 IA-2(256-760) or 35S IA-2IC proteins, samples were processed with the usual radioimmunoprecipitation assay. An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody. IEDB IEDB radio immuno assay An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay. Bjoern Peters Melanie Courtot RRT-PCR RT-rt PCR qRT-PCR real time reverse-transcription polymerase chain reaction assay Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes. A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest. IEDB IEDB X-ray crystallography 3D molecular structure determination assay A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color. An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene. IEDB IEDB promoter activity detection by reporter gene assay nasopharyngeal aspirate specimen type of sample used in the PCIRN influenza network A specimen which derives from nasopharyngeal mucosa after aspiration. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasopharyngeal aspirate specimen freezing storage a fozen pellet used for later assay A storage process in temperature that maintenance the frozen status of the stored entities. 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 2014/2/3 OBI dev call: "prepare for maintenance" is a separate process. For example, 'freezing' and 'flash freezing' are defined and can be used to produce frozen material for storage. Updated both textual and logical definition. Both input and output material of freezing storage have quality frozen. Person: Alan Ruttenberg, Mathias Brochhausen MO_481 frozen_storage OBI freezing storage Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody. A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution. IEDB FACS IEDB flow cytometry assay nasal swab specimen type of sample used in the PCIRN influenza network A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of exudate and epithelial debris for microbiological or cellular examination. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasal swab specimen Dulbecco's modified Eagle medium A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. Logical definition should contain all components listed in textual definition at some point. PERSON:Bjoern Peters D-MEM DMEM Dulbecco's modified Eagle medium animal euthanization Rats were euthanized with CO2 A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject Helen Parkinson and Melissa Haendel animal sacrifice Melissa Haendel may later be refined with more specific list of organisms animal euthanization Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture. An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest. IEDB Luminex assay IEDB cytometric bead array assay labeled RNA extract a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments. Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group. Added duirng Mar 1, 2010 dev call Group: OBI group Group: OBI group labeled RNA extract frozen specimen Frozen blood plasma A specimen that has been frozen in order to store it. Person:Alan Ruttenberg MO_610 frozen_sample frozen specimen Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow. A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction. IEDB IEDB surface plasmon resonance binding assay labeled specimen A specimen that has been modified in order to be able to detect it in future experiments added during call 3/1/2010 OBI group labeled specimen infectious agent is a material entity bearing the disposition to infect an organism IEDB IEDB infectious agent obsolete_ambidexterious handedness true lyophilization storage a storage process with input material entity and output freeze dried material for long time storage PERSON: Chris Stoeckert PERSON: Jie Zheng can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed lyophilization storage material combination function A stirrer has a material combination function A material separation function is a function that decreases the resolution between two or more material entities. Helen Parkinson OBI material combination function EBI provides training on databases and tools and has a training service provider role a service provider role which is realized by a servicer provider organization performing some training PERSON:Helen Parkinson OBI obsolete_training service provider role true calorimeter A measurement device that is used to calculate the heat flow of a chemical reaction or physical change. PERSON:Bjoern Peters calorimetry instrument? http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm calorimeter study intervention A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study. PERSON: Bjoern Peters GROUP: OBI study intervention material separation device flow cytometer A device with a separation function realized in a planed process material separation device positron emission tomography scanner A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. PERSON:Bjoern Peters PET scanner? http://en.wikipedia.org/wiki/Positron_emission_tomography positron emission tomography scanner intramuscular injection is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe intramuscular injection micromanipulator A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand. PERSON:Bjoern Peters http://en.wikipedia.org/wiki/Micromanipulator micromanipulator A person or organization who provides access to a DNA sequencer. a service provider role which is realized by a servicer provider organization performing access to some material PERSON:Helen Parkinson OBI obsolete_material access provider role true obsolete_left handedness true categorical measurement datum A measurement datum that is reported on a categorical scale. Bjoern Peters nominal mesurement datum Bjoern Peters categorical measurement datum training process e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility a process that achieves a training objective training process optical microscope A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range PERSON:Bjoern Peters optical microscope service consumer role A biologist who uses a sequencing services fulfills the role of a service consumer a role which inheres in a person who uses a service Person:Helen Parkinson OBI service consumer role intradermal injection is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot intradermal injection chemical cleavage PMID: 20171258. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG. Biochimie. 2010 Feb 18. chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent PERSON:Philippe Rocca-Serra RNA ontology group chemical cleavage The Edinburgh handedness assay is a specific method of determing handedness An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure. Helen Parkinson handedness test url:http://en.wikipedia.org/wiki/Handedness handedness assay vibration isolation table A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor. PERSON:Bjoern Peters United States Patent 6877711 vibration isolation table sterilization function a function to remove viable organisms from an input material sterilization function service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role oscilloscope A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis). PERSON:Bjoern Peters http://en.wikipedia.org/wiki/Oscilloscope oscilloscope accessed material role the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism is realized in a planned process where the bearer participates AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it accessed material role paraffin specimen liver tissue embedded in paraffin a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin PERSON: Chris Stoeckert PERSON: Jie Zheng MO_990 paraffin_sample paraffin specimen compound treatment design an intervention design in which the treatment is the administration of a compound This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc. PERSON: Bjoern Peters MO_555 compound_treatment_design compound treatment design oral administration An administering substance in vivo into the mouth of an organism PERSON: Melanie Courtot oral administration processed specimen A specimen that has been intentionally physically modified. A tissue sample that has been sliced and stained for a histology study. Bjoern Peters Bjoern Peters processed specimen subcutaneous injection is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot subcutaneous injection electrode puller A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube. PERSON:Bjoern Peters http://faculty.plattsburgh.edu/donald.slish/Puller1.html electrode puller obsolete_handedness true An assay where a person makes a statement that indicates what handedness he has from a choice of different categories. self reported handedness assessment vibrotome A preparation device that uses a vibrating razor blade to cut through tissue. vibrotome reagent application function An automatic tissue processor automatically applies antibodies and buffers to histological tissue preparations. A function that is realized when a reagent is automatically added to some research material. PERSON: Nicole Vasilevsky, Matthew Brush PERSON: Nicole Vasilevsky, Matthew Brush 4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people? reagent application function addition of molecular tracer function Immunohistochemical labeling of tissue sections by an autostainer staining system. A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen. PERSON: Nicole Vasilevsky, Matthew Brush PERSON: Nicole Vasilevsky, Matthew Brush addition of molecular tracer function training objective A training objective is fulfilled by e.g. a bioconductor tutorial which instructs the user in the use of a package An objective specification which is fulfilled by the provision of some training. Helen Parkinson OBI training objective categorical label The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label An assay in which a measurement is made by observing entities located in a live cell. in live cell assay lyophilized specimen freezing dried DNA a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. PERSON: Chris Stoeckert PERSON: Jie Zheng MO_589 freeze_dried_sample lyophilized specimen Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. An assay in which a measurement is made by observing entities located in an organism. Bjoern Peters in vivo assay in live organism assay container A device that can be used to restrict the location of material entities over time 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?) PERSON: Bjoern Peters container A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. obsolete device true dose specification a protocol specifying to administer 1 ml of vaccine to a mouse a directive information entity that describes the dose that will be administered to a target dose specification 1 scalar score from composite inputs A measurement datum which is the result of combining multiple datum. For example, a mean or summary score. JT: We included this because we wanted to talk about an output from a questionnaire that summarized the answers to the questionnaire, but which was not actually the answer to any single question. Person: Jessica Turner questionaire score Person: Jessica Turner JZ: can we defined it logically as the output of some data transformation, like aggragate data transformation? scalar score from composite inputs fresh specimen a liver freshly removed from a rat a specimen that is output of a specimen creation process used for an investigation without storage. PERSON: Chris Stoeckert PERSON: Jie Zheng MO_730 fresh_sample fresh specimen a processed material created to have a function and which requires electrical power to execute obsolete_electrically powered device true sequence data example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. A data item that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. Person:Chris Stoeckert GROUP: OBI sequence data obsolete_right handedness true Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates. A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels. IEDB IEDB cell-cell binding detection by flow cytometry assay handedness categorical measurement datum A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally PERSON:Alan Ruttenberg PERSON:Jessica Turner handedness categorical measurement datum paraffin storage a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group need to specify paraffin or wax is one of specified input of the process paraffin storage An assay in which a measurement is made by observing entities located in a container. in container assay DNA sequencing of a sample by a core lab which returns data to the consumer a service provider role which is realized by a servicer provider organization performing a protocol execution PERSON:Helen Parkinson obsolete_protocol service provider role true agar stab specimen a specimen that is output of a process that cell culture inoculated into agar for long term storage. PERSON: Chris Stoeckert PERSON: Jie Zheng MO_971 agar_stab agar stab specimen computed tomography scanner An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation. PERSON:Bjoern Peters CT scanner X-ray computed tomography scanner http://en.wikipedia.org/wiki/X-ray_computed_tomography computed tomography scanner intranasal mucosal administration The administration of a substance into the intranasal mucosis of an organism PERSON: Melanie Courtot intranasal mucosal administration dose An organism has been injected 1ml of vaccine A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. dose growth condition intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing PERSON: Bjoern Peters MO_588 growth_condition_design growth condition intervention design A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments obsolete_DNA sequencing training service true obsolete_general scalar measurement datum true Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache. The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis https://github.com/obi-ontology/obi/issues/623 obsolete performing a diagnosis true PCR instrument A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent. PCR instrument electron microscope A microscope that produces an image of an object by targeting it with an electron beam electron microscope 1 Edinburgh score A score that measures the dominance of a person's right or left hand in everyday activities. Person: Alan Ruttenberg Person:Jessica Turner PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113 WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html Edinburgh score DNA sequencing service A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized. Eagle-i will supply better English definition DNA sequencing service service provision objective A sequencing centre has a service provision objective An objective which is fulfilled by the provision of some service e.g. a training service Helen Parkinson OBI service provision objective intravenous injection is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe PERSON: Melanie Courtot intravenous injection administration of material to specimen Staining cells in a tissue slice with a dye. The directed combination of a material entity with a specimen. Bjoern Peters Bjoern Peters administration of material to specimen device creation objective an objective which aims to create a device with a specified function PERSON: Helen Parkinson OBI device creation objective growth environment The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth. Right now this may be incomplete. Should also cover e.g. sound, light as well. PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters OBI group growth environment questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster questionnaire Verdino (1998) Perceptual and Motor Skills. 86 (2): 476_8. (PMID: 9638746) uses this measure in an experimental study: "Individuals of extreme handedness based on the Edinburgh Handedness Inventory (laterality Quotients of +90 to +100 and -100 and +54; 50 each)" An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand. Alan Ruttenberg Gully Burns (orcid:0000-0003-1493-865X) Jessica Turner PMID:5146491 url:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory Edinburgh handedness assay Faraday cage A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields. PERSON:Bjoern Peters Faraday shield Wikipedia http://en.wikipedia.org/wiki/Faraday_cage isolation function? HP Faraday cage agar stab storage a storage process with input cell culture and agar and output agar stab for long time storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group need to specify that agar is one of input for this process agar stab storage PMID:16453415 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse CL3 RNA ontology RNASE CL3 structure mapping assay PMID:2422386 and PMID:2446263 A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Philippe Rocca-Serra single nucleotide resolution mapping assay using CMCT probe RNA ontology CMCT structure mapping assay image acquisition Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel A planned process that captures an image of an object. PERSON: Jie Zheng image acquisition image creation PMID:6209709 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using Fe-MP probe RNA ontology MPE-Fe(II) structure mapping assay A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum obsolete_qualitative binding detection assay true nucleic acid extract An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen. Person: Jie Zheng UPenn Group nucleic acid extract PMID:7002606 and PMID:2446263 A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe Philippe Rocca-Serra single nucleotide resolution mapping assay using ENU probe RNA ontology ENU structure mapping assay PMID:7031604 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse V1 RNA ontology RNASE V1 structure mapping assay single nucleotide resolution mapping assay using Kethoxal probe A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe Philippe Rocca-Serra RNA ontology kethoxal structure mapping assay A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes. Philippe Rocca-Serra RNAO and OBI https://github.com/obi-ontology/obi/issues/808 single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing PMID:6159633 and PMID:2446263 A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe Philippe Rocca-Serra single nucleotide resolution mapping assay using DMS probe RNA Ontology DMS structure mapping assay PMID:3773731 A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure Philippe Rocca-Serra DNAse footprinting assay single nucleotide resolution mapping assay using DNAse I RNA ontology DNASE 1 structure mapping assay A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes. Philippe Rocca-Serra RNAO and OBI single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing PMID:2843807 A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using Rhodium probe RNA ontology Rhodium DNA structure mapping assay PMID:7527340 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using RNA adenosine deaminase I RNA ontology RNA ADA I RNA structure mapping assay PMID:2686708 A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe Philippe Rocca-Serra single nucleotide resolution mapping assay using Lead probe RNA ontology Lead structure mapping assay PMID:6207483 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse T2 RNA ontology RNASE T2 structure mapping assay An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene. Bjoern Peters David Osumi Sutherland gene dosage assay PMID: 7862644 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using Fe-BABE probe RNA ontology Fe-BABE RNA structure mapping assay PMID:409999 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse U2 RNA ontology RNASE U2 structure mapping assay Determination of KD value for an antibody binding a protein using a BIACORE assay. A binding assay where the specified output is a binding constant Bjoern Peters Jason Greenbaum Randi Vita IEDB binding constant determination assay PMID: 15796531 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe Philippe Rocca-Serra SHAPE mapping assay single nucleotide resolution mapping assay using NMIA probe RNA ontology NMIA RNA structure mapping assay PMID:10772868 A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe Philippe Rocca-Serra single nucleotide resolution mapping assay using Terbium probe RNA ontology Terbium RNA structure mapping assay feature extraction A planed process with objective of obtaining quantified values from an image. PERSON: Jie Zheng MO_928: feature_extraction feature extraction PMID:2501870 A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe Philippe Rocca-Serra MOHCA assay OH footprinting assay single nucleotide resolution mapping assay using OH-radical probe RNA ontology OH-radical structure mapping assay PMID:114514 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using RNAse T1 RNA ontology RNASE T1 structure mapping assay array image acquisition An image creation process that generate an image from the array. PERSON: Jie Zheng array image acquisition MO_929: image_acquisition array image creation light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) A device which has a function to emit light. Person:Helen Parkinson OBI light emission device perturbation device A homogenizer is a perturbation device. A perturbation device is a device which is designed to perform a perturb function Helen Parkinson OBI Vancouver workshop 2010 PERSON: Helen Parkinson perturbation device environmental control device A growth chamber is an environmental control device. An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. Helen Parkinson OBI environmental control device PMID:363143 A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe. Philippe Rocca-Serra single nucleotide resolution mapping assay using Nuclease S1 RNA ontology Nuclease S1 structure mapping assay specimen fixation function e.g the function of a bar code reader used to read slide bar codes a function that allows specific identification of individual speciment from one another. EAGLE-I specimen fixation function A specimen fixation function is a function that holds or fastens an entity in a fixed position. EAGLE-I obsolete_specimen fixation function true PMID:3016894 A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe Philippe Rocca-Serra RNA Ontology Ruthenium structure mapping assay PMID:10573122 and PMID: 18369975 A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity Philippe Rocca-Serra RNA ontology inline probing RNA structure mapping assay current amplification function A current amplification function is an amplification function that increases the amplitude of a current. EAGLE-I current amplification function stabilization function A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity. EAGLE-I isolation function stabilization function pump function a transfer unction where the transfer requires work to move the entity, often against a gradient. EAGLE-I pump function cell transfer function A cell harvester has a cell transfer function. is a transfer function that displaces cells from one place to another EAGLE-I cell transfer function angiograph A device that records the patterns of pulse waves inside blood vessels. PERSON: Erik Segerdell http://medical-dictionary.thefreedictionary.com/angiograph angiograph capillary blotter A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed. PERSON: Erik Segerdell http://www.biometra.de/ capillary blotter bioreactor A device or system that supports a biologically active environment. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Bioreactor bioreactor pH meter A device that is used to measure the pH (acidity or alkalinity) of a liquid. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/PH_meter pH meter digital camera An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Digital_camera digital camera chip spotting device A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray. PERSON: Erik Segerdell United States Patent 7416705 chip spotting device RNA extraction/purification instrument A device that is used to isolate and collect RNA for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell RNA extraction/purification instrument DNA extract The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Person: Jie Zheng Group: UPenn group DNA extract two-photon laser/detector A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy two-photon laser/detector electrophoresis system A device that moves charged particles through a medium by using an electric field induced by electrodes. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Category:Electrophoresis electrophoresis system PET synthesizer A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography. PERSON: Erik Segerdell PERSON: Erik Segerdell PET synthesizer spinning-disk confocal microscope A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Nipkow_disk spinning-disk confocal microscope DNA synthesizer An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides. PERSON: Erik Segerdell http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers DNA synthesizer high performance liquid chromatography instrument A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/High_performance_liquid_chromatography high performance liquid chromatography instrument microplate reader A measurement device that detects biological, chemical or physical events of samples in microtiter plates. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Plate_reader microplate reader ELISA microplate reader A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA). PERSON: Erik Segerdell PERSON: Erik Segerdell ELISA microplate reader spot cutter A robotic device that is used to excise spots from gels. PERSON: Erik Segerdell PERSON: Erik Segerdell spot cutter microwave synthesis system A device that is used to apply microwave irradiation to chemical reactions. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Microwave_chemistry microwave synthesis system densitometer A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Densitometer densitometer automatic staining machine A device that is used to automatically stain tissue sections on slides or tissue specimens. PERSON: Erik Segerdell PERSON: Erik Segerdell automatic staining machine automatic tissue processor A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue. PERSON: Erik Segerdell United States Patent 3762362 automatic tissue processor stereo microscope An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope stereo microscope top loading balance A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass. PERSON: Erik Segerdell PERSON: Erik Segerdell top loading balance perfusion station A device or system in which perfusion units are integrated. PERSON: Erik Segerdell PERSON: Erik Segerdell perfusion station SPECT scanner A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography SPECT scanner array manufacturer role a manufacturer role which is played by the person or organization that manufactured the array PERSON: Chris Stoeckert, Jie Zheng MO_695 array_manufacturer array manufacturer role scintillation counter A device that is used to measure ionizing radiation. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Scintillation_counter scintillation counter programmable array microscope A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures. PERSON: Erik Segerdell Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8 programmable array microscope cryostat A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Cryostat cryostat microtome knife maker A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy. PERSON: Erik Segerdell PERSON: Erik Segerdell microtome knife maker cryofixation device A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Cryofixation cryofixation device hybridization oven A device that creates an appropriate environment for nucleic acid hybridization. PERSON: Erik Segerdell PERSON: Erik Segerdell hybridization oven incubator shaker An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). PERSON: Erik Segerdell PERSON: Erik Segerdell incubator shaker small-animal image acquisition device A device that is used to image small laboratory animals (e.g., rats and mice) in vivo. PERSON: Erik Segerdell PERSON: Erik Segerdell small-animal image acquisition device infrared image acquisition device An image acquisition device that is responsive to an infrared emissive target within a given field of view. PERSON: Erik Segerdell United States Patent 4107530 infrared image acquisition device confocal microscope A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Confocal_microscopy confocal microscope patch clamp device A device used in electrophysiology that allows the study of single or multiple ion channels in cells. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Patch_clamp patch clamp device gel imaging system A device that is used to acquire images of laboratory gels. PERSON: Erik Segerdell PERSON: Erik Segerdell gel imaging system protein separation apparatus A device that is used for the separation of proteins. PERSON: Erik Segerdell PERSON: Erik Segerdell protein separation apparatus multichannel electronic pipette A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations. PERSON: Erik Segerdell http://www.faqs.org/patents/app/20090196797 multichannel electronic pipette vitrification apparatus A device that is used to effect the transition of a substance into a glass. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Glass_transition vitrification apparatus radiography instrument An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Medical_radiography radiography instrument radiation measurement device A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector. PERSON: Erik Segerdell PERSON: Erik Segerdell radiation measurement device lyophilizer A device that is used to freeze dry material. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Freeze_drying lyophilizer tandem mass spectrometer A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge. PERSON: Erik Segerdell http://goldbook.iupac.org/T06250.html tandem mass spectrometer microhardness tester A hardness testing device that is used in light-optical microscopes. PERSON: Erik Segerdell United States Patent 4611487 microhardness tester multimode microplate reader A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence. PERSON: Erik Segerdell PERSON: Erik Segerdell multimode microplate reader mechanical balance A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight). PERSON: Erik Segerdell http://www.britannica.com/EBchecked/topic/49765/balance mechanical balance computer cluster A group of linked computers, working together closely so that in many respects they form a single computer. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Cluster_(computing) computer cluster microtome knife sharpener A device that is used to sharpen knives used in microtomy. PERSON: Erik Segerdell PERSON: Erik Segerdell microtome knife sharpener plate shaker A device that provides shaking motion for microplates. PERSON: Erik Segerdell PERSON: Erik Segerdell plate shaker coagulation analyzer A device for automatically analyzing blood coagulation in a clinical laboratory. PERSON: Erik Segerdell United States Patent 5439646 coagulation analyzer laser capture microdissection microscope A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue. PERSON: Erik Segerdell http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine laser capture microdissection microscope liquid extraction robot A liquid handling device that provides automatic liquid extraction. PERSON: Erik Segerdell PERSON: Erik Segerdell liquid extraction robot ultrasound machine A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Sonography ultrasound machine immunoblot scanner A device that is used for the imaging of immunoblots. PERSON: Erik Segerdell PERSON: Erik Segerdell immunoblot scanner microcentrifuge A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Laboratory_centrifuge microcentrifuge electronic repeater pipette A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations. PERSON: Erik Segerdell http://www.faqs.org/patents/app/20090196797 electronic repeater pipette electron paramagnetic resonance spectrometer An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance electron paramagnetic resonance spectrometer rocker A device that provides three-dimensional motion for biomedical applications (e.g., gel trays). PERSON: Erik Segerdell PERSON: Erik Segerdell rocker analytical balance A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Weighing_scale analytical balance scanning force microscope A microscope that forms images of surfaces using a physical probe that scans the specimen. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Scanning_probe_microscopy scanning force microscope pulsed-field gel electrophoresis system A gel electrophoresis system in which the gel matrix is subjected to an electric field that periodically changes direction. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis pulsed-field gel electrophoresis system tissue embedding station A device that is used to perform paraffin embedding of tissue specimens. PERSON: Erik Segerdell PERSON: Erik Segerdell tissue embedding station nucleic acid sequencer An device that is used to determine the order of nucleotides in nucleic acid sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid sequencer bead array reader A device that is used to acquire and image bead array data. PERSON: Erik Segerdell PERSON: Erik Segerdell bead array reader real-time PCR machine An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction real-time PCR machine paraffin oven A device that is used for the warming of paraffin embedding medium. PERSON: Erik Segerdell PERSON: Erik Segerdell paraffin oven autoclave A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents. PERSON: Erik Segerdell J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave autoclave microplate washer A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY?? PERSON: Erik Segerdell http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037 microplate washer nucleic acid extraction/purification instrument A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid extraction/purification instrument ELISA microplate washer A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA). PERSON: Erik Segerdell PERSON: Erik Segerdell ELISA microplate washer vacuum manifold A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY. PERSON: Erik Segerdell PERSON: Erik Segerdell vacuum manifold DNA extraction/purification instrument A device that is used to isolate and collect DNA for subsequent molecular analysis. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/DNA_extraction DNA extraction/purification instrument multichannel pipette A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications. PERSON: Erik Segerdell PERSON: Erik Segerdell multichannel pipette cell harvester A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT? PERSON: Erik Segerdell PERSON: Erik Segerdell cell harvester portable fluorometer A compact fluorometer that can be carried or moved with ease. PERSON: Erik Segerdell PERSON: Erik Segerdell portable fluorometer gel electrophoresis system An electrophoresis system in which an electric field is applied to a gel matrix PERSON: Erik Segerdell https://en.wikipedia.org/wiki/Gel_electrophoresis gel electrophoresis system diffractometer A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Diffractometer diffractometer microdissection instrument A device that is used for the dissection of tissues under magnification. PERSON: Erik Segerdell http://medical-dictionary.thefreedictionary.com/microdissection microdissection instrument micropipette puller A device that is used to fabricate glass micropipettes. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Micropipette micropipette puller laser scanning confocal microscope A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy laser scanning confocal microscope digital microscope A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Digital_microscope digital microscope freeze substitution system A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins. PERSON: Erik Segerdell doi:10.1017/S143192760707866X freeze substitution system micropipette A microinjection device that is used to measure very small volumes of liquids. PERSON: Erik Segerdell http://www.answers.com/topic/micropipette micropipette voltage clamp device A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Voltage_clamp voltage clamp device vacuum oven A device that heats materials in a vacuum. PERSON: Erik Segerdell PERSON: Erik Segerdell vacuum oven slide warmer A device that is used to heat microscope slides. PERSON: Erik Segerdell PERSON: Erik Segerdell slide warmer capillary electrophoresis instrument An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Capillary_electrophoresis capillary electrophoresis instrument denaturing high-performance liquid chromatography instrument A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis. PERSON: Erik Segerdell doi:10.1385/1-59259-850-1:173 denaturing high-performance liquid chromatography instrument agarose gel electrophoresis system A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis agarose gel electrophoresis system balance A measuring instrument that is used to determine the weight or mass of an object. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Weighing_scale balance surface plasmon resonance instrument A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Surface_plasmon_resonance surface plasmon resonance instrument protein sequencer An device that is used to determine the order of amino acids in protein sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell protein sequencer X-ray source A device that is used to generate X-rays. PERSON: Erik Segerdell x-ray generator http://en.wikipedia.org/wiki/X-ray_generator X-ray source liquid chromatography instrument A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated PERSON: Matthew Brush PERSON: Matthew Brush liquid chromatography instrument spike-in quality control role a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter MO_937 spike_quality_control spike-in quality control role individual organism identifier a CRID symbol used to distinguish one individual organism from another. PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual individual organism identifier dye swap quality control role a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes PERSON: Chris Stoeckert, Jie Zheng MO_524 dye_swap_quality_control dye swap quality control role labeled nucleic acid extract a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments. Person: Jie Zheng labeled extract MO_221 labeledExtract labeled nucleic acid extract binding constant The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes". A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed. 10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum binding constant Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody. A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration. IEDB IEDB 3D structure determination of bound molecular complex assay Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen. The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. An assay with the objective to characterize the disposition of two or more material entities to form a complex. Bjoern Peters Jason Greenbaum Randi Vita binding assay cell culture expansion a process that results in the increase of cell numbers including grow of yeast and bacteria PERSON: Chris Stoeckert, Jie Zheng MO_758 grow BP: add it as subclass of 'cell culturing' JZ: No 'cell culturing' in OBI Has term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process. cell culture expansion gene knock out a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods. PERSON: Chris Stoeckert, Jie Zheng MO_771 gene_knock_out gene knock out gene knock in a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion. PERSON: Chris Stoeckert, Jie Zheng MO_437 gene_knock_in WEB: http://en.wikipedia.org/wiki/Gene_Knock-in gene knock in chromosomal substitution A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'. PERSON: Chris Stoeckert, Jie Zheng MO_995 chromosomal_substitution chromosomal substitution genetically modified material a material entity, organism or cell, that is the output of a genetic transformation process. PERSON: Jie Zheng GROUP: OBI term is proposed by BP on Oct 25, 2010 dev call genetically modified material transfection a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell PERSON: Chris Stoeckert, Jie Zheng MO_366 transfection transfection genetic transformation objective a material transformation objective aims to create genetically modified organism or cell Person: Jie Zheng Person: Jie Zheng suggested to be added by BP and AR during Oct 25, 2010 dev call genetic transformation objective induced mutagenesis A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation. Label and definition were clarified as per https://github.com/obi-ontology/obi/issues/1366 PERSON: Chris Stoeckert, Jie Zheng MO_564 induced_mutation induced mutagenesis 3D structural organization datum The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. A measurement datum that describes the structural orientation of a material entity in 3D space. PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters 3D structural organization datum age since planting measurement datum An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing. PERSON:Chris Stoeckert, Jie Zheng MO_495 planting Discussed by Jie and Chris, proposed to combine with different kinds of processes as initial time point. Proposed 'age measurement assay' is proceeded by some process. The process can be any kind of process defined in OBI. Think it is more flexible. However, it is hard to model due to lake of temporal predicates on Nov 15, 2010 dev call. Term proposed by Bjoern on Nov 8, 2010 dev call Supported by Alan on Nov 15, 2010 dev call age since planting measurement datum age since hatching measurement datum An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg. PERSON:Chris Stoeckert, Jie Zheng MO_745 hatching age since hatching measurement datum An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted). This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature. Alan Ruttenberg age measurement assay OBI group age determination assay age since egg laying measurement datum An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism. PERSON:Chris Stoeckert, Jie Zheng MO_767 egg laying age since egg laying measurement datum assay validation objective an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results PERSON: Chris Stoeckert, Jie Zheng GROUP: Penn Group assay validation objective age since germination measurement datum An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. PERSON:Chris Stoeckert, Jie Zheng MO_590 germination age since germination measurement datum validation by reverse transcription PCR design a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results PERSON: Chris Stoeckert, Jie Zheng MO_986 reverse_transcription_PCR_quality_control validation by reverse transcription PCR design age since eclosion measurement datum An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. PERSON:Chris Stoeckert, Jie Zheng MO_876 eclosion age since eclosion measurement datum age since sowing measurement datum An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. PERSON:Chris Stoeckert, Jie Zheng MO_748 sowing age since sowing measurement datum age since coitus measurement datum An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. PERSON:Chris Stoeckert, Jie Zheng MO_783 coitus age since coitus measurement datum validation by real time PCR design a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results PERSON: Chris Stoeckert, Jie Zheng MO_434 real_time_PCR_quality_control validation by real time PCR design age measurement datum A time measurement datum that is the result of measurement of age of an organism note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage. PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng MO_178 Age In MageTab file, we use initialTimePoint (a process) + age (a number expected) + TimeUnit (definied in UO, such as year, hour, day, etc.) Now we use the term label indicating the start time point of measuring the age, (number + TimeUnit) are expected instances of the class discussed on Nov 15, dev call All subtype will be defined by textual definition now. age measurement datum age since fertilization measurement datum An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. Definition of fertilization comes from GO. PERSON:Chris Stoeckert, Jie Zheng MO_701 fertilization age since fertilization measurement datum age since birth measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. PERSON:Chris Stoeckert, Jie Zheng MO_710 birth age since birth measurement datum An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. Chris Stoeckert Jie Zheng Penn Group reverse transcription polymerase chain reaction assay half life datum (t 1/2) The time it takes for 50% of a class of stochastic processes to occur. Bjoern Peters t 1/2 Bjoern Peters half life datum (t 1/2) dose response curve A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve. Bjoern Peters; Randi Vita dose response curve service providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony. A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. Carlo; Matt OBI workshop San Diego 2011 service passive immunization Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox. Transferring epitope specific T cells from one mouse into another. The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens. PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum adoptive transfer passive immunization selective organism creation objective an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms. PERSON: Chris Stoeckert, Jie Zheng WEB: wikipedia http://en.wikipedia.org/wiki/Cultivar http://en.wikipedia.org/wiki/Ecotype http://en.wikipedia.org/wiki/Strain_%28biology%29 selective organism creation objective Individual epitope immunization in vivo Injection of a peptide T cell epitope into a mouse An immunization in which an individual epitope is administered into a host organism. 3/16/11 BP: This should have as a logical definition the exclusion that the immunogen cannot be something beyond the epitope itself. I don't know if that is possible to do here. PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita Individual epitope immunization in vivo An assay that determines the sequence of an RNA molecule. Bjoern Peters Bjoern Peters RNA sequencing assay An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism. Bjoern Peters efficacy of in vivo intervention efficacy of epitope intervention experiment An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed. Bjoern Peters protection from infectious challenge epitope protection from infectious challenge experiment half maximal effective concentration (EC50) Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed. half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time. Bjoern Peters; Randi Vita wikipedia half maximal effective concentration (EC50) binding datum A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is. Bjoern Peters; Randi Vita binding datum negative binding datum A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex. negative binding datum An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed. Bjoern Peters protection from tumor challenge epitope protection from tumor challenge experiment An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host. Bjoern Peters protection from challenge epitope protection experiment selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert cultivar ecotype strain MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar selectively maintained organism An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls. Bjoern Peters burden after infectious challenge epitope protection from infectious challenge experiment based on pathogen burden Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers; PCR amplification using primers specific for influenza virus. An assay that measures the presence or amount of an infectious agent in an evaluant Bjoern Peters Jason Greenbaum Randi Vita Richard Scheuermann infectious agent detection assay An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host. Bjoern Peters exacerbation assay epitope disease exacerbation experiment An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host. Bjoern Peters host survival after challenge epitope protection experiment based on survival An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host. Bjoern Peters decreased disease symptoms after treatment epitope treatment experiment half maximal inhibitory concentration (IC50) Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited. Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect. Bjoern Peters; Randi Vita wikipedia half maximal inhibitory concentration (IC50) epitope specific immune intervention An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope Person: Bjoern Peters, Randi Vita, Jason Greenbaum epitope specific immune intervention epitope specific cytokine production by T cells A process of cytokine production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific cytokine production by T cells An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|ELISPOT ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells operator variation design A study design that assesses the operator performance and relation to data consistency and quality. Person: Chris Stoeckert, Jie Zheng MO_519 operator_variation_design operator variation design A cytometric bead array assay that detects IP-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|cytometric bead array cytometric bead array assay measuring epitope specific IP-10 production by T cells comparative genome hybridization by array design A study design that detects genomic copy number variations using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_856 comparative_genome_hybridization_design comparative genome hybridization by array design A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|biological activity assay measuring epitope specific interleukin-27 production by T cells A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. Person: Chris Stoeckert, Jie Zheng MO_454 in_vivo_design in vivo design genotyping by high throughput sequencing design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping by high throughput sequencing design epitope specific tolerance induction by T cells A process of tolerance induction by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific tolerance induction by T cells innate behavior design A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. Person: Chris Stoeckert, Jie Zheng MO_355 innate_behavior_design innate behavior design A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells SNP microarray A DNA microarray used to detect polymorphisms in DNA samples Person: Helen Parkinson EFO_0002703 SNP array SNP microarray cell component comparison design A study design that compares samples from different cell components. Person: Chris Stoeckert, Jie Zheng MO_1019 cell_component_comparison_design cell component comparison design An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|ELISPOT ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells epitope specific macrophage inflammatory protein-1 alpha production by T cells A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific macrophage inflammatory protein-1 alpha production by T cells epitope specific T cell activation A process of T cell activation resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific T cell activation A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-10 release|biological activity assay measuring epitope specific interleukin-10 production by T cells A cytometric bead array assay that detects transforming growth factor-beta production by T cells PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|cytometric bead array cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells ex vivo design A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment. Person: Chris Stoeckert, Jie Zheng MO_808 ex_vivo_design ex vivo design epitope specific type IV hypersensitivity by T cells A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific type IV hypersensitivity by T cells normalization testing design A study design that tests different normalization procedures. Person: Chris Stoeckert, Jie Zheng MO_729 normalization_testing_design normalization testing design A flow cytometry assay that detects epitope specific perforin release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB perforin release|intracellular staining intracellular material detection assay measuring epitope specific perforin release A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-22 release|biological activity assay measuring epitope specific interleukin-22 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-8 release|biological activity assay measuring epitope specific interleukin-8 production by T cells epitope specific chemokine (C-C motif) ligand 1 production by T cells A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific chemokine (C-C motif) ligand 1 production by T cells A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-10 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin ArrayExpress production team EFO:0002764 ChIP-chip by SNP array assay An enzyme-linked immunosorbent assay that detects RANTES production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|ELISA ELISA measuring epitope specific RANTES production by T cells A cytometric bead array assay that detects interleukin-1 beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1b release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells genetic population background information genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information a genetic characteristics information which is a part of genotype information that identifies the population of organisms proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic population background information environmental history design A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc. Person: Chris Stoeckert, Jie Zheng MO_698 environmental_history_design environmental history design An enzyme-linked immunospot assay that detects interleukin-6 production by T cells PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-6 production by T cells A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response. IEDB IEDB antibody help|in vivo assay in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|surface plasmon resonance (SPR)|nM plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|biological activity assay measuring epitope specific interleukin-5 production by T cells An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|ELISA ELISA measuring epitope specific transforming growth factor-beta production by T cells A T cell epitope specific cytokine production assay that detects RANTES production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|biological activity assay measuring epitope specific RANTES production by T cells A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|biological activity assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells epigenetic modification identification objective A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications. Chris Stoeckert, Jie Zheng Person: Chris Stoeckert epigenetic modification identification objective A transcription profiling by array assay that uses a tiling path array. James Malone EFO:0002769 transcription profiling by tiling array assay An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-22 release|ELISA ELISA measuring epitope specific interleukin-22 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|biological activity assay measuring epitope specific interleukin-21 production by T cells An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-9 release|ELISA ELISA measuring epitope specific interleukin-9 production by T cells A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team transcription profiling by high throughput sequencing design A flow cytometry assay that detects interleukin-6 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|cytometric bead array cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|ELISA ELISA measuring epitope specific interleukin-23 production by T cells A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB perforin release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNF release|ELISA ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells A genotyping assay that uses a high througput sequencer James Malone EFO:0002771 genotyping by high throughput sequencing assay An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin Bjoern Petesr James Malone ChIP-on-chip assay url:http://en.wikipedia.org/wiki/ChIP-on-chip ChIP-chip assay epitope specific T cell tolerance induction A process of T cell tolerance induction resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific T cell tolerance induction An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) T cell degranulation by intracellular staining obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation true A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-13 release|biological activity assay measuring epitope specific interleukin-13 production by T cells array platform variation design A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. Person: Chris Stoeckert, Jie Zheng MO_899 array_platform_variation_design array platform variation design A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-9 release|biological activity assay measuring interleukin-9 production by T cells epitope specific interleukin-3 production by T cells A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-3 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells epitope specific lymphotoxin A production by T cells A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific lymphotoxin A production by T cells epitope specific interleukin-1 alpha production by T cells A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-1 alpha production by T cells ChIP-seq design A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications. Person: Chris Stoeckert, Jie Zheng http://en.wikipedia.org/wiki/Chip-Sequencing ChIP-seq design translational bias design A study design that characterizes the association of transcripts and translation machinery. Person: Chris Stoeckert, Jie Zheng MO_939 translational_bias_design translational bias design An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|ELISA ELISA measuring epitope specific interleukin-3 production by T cells An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|ELISA ELISA measuring epitope specific interleukin-1 alpha production by T cells epitope specific interleukin-27 production by T cells A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-27 production by T cells A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB T cell help|in vivo assay in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|biological activity assay measuring epitope specific transforming growth factor-beta production by T cells FWER adjusted p-value http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests PERS:Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate) FWER adjusted p-value A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology ArrayExpress production team Helen Parkinson James Malone EFO:0002761 DNA methylation profiling by high throughput sequencing assay epitope specific transforming growth factor-beta production by T cells A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific transforming growth factor-beta production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB degranulation|biological activity assay measuring epitope specific cytotoxic T cell degranulation A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TGFb release|bioassay cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells A type of transcription profiling assay where transcripts are extracted from a sample, usually (but not always) transformed into cDNA, and then sequenced. Sequence reads are generally mapped to a reference and quantified to establish levels of gene transcription. Michelle Giglio Sebastian Duesing RNA-seq assay transcription profiling by RNA sequencing assay An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNF release|ELISPOT ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells A genotyping assay that uses an array ArrayExpress production team EFO:0002767 genotyping by array assay epitope specific interleukin-16 production by T cells A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-16 production by T cells A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|biological activity assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells DNA methylation profiling by array design A study design in which the methylation state of DNA is determined and is compared between samples using array technology. Person: Chris Stoeckert, Jie Zheng GROUP: ArrayExpress production team DNA methylation profiling by array design A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-22 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|biological activity assay measuring epitope specific interleukin-16 production by T cells An enzyme-linked immunosorbent assay that detects IP-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|ELISA ELISA measuring epitope specific IP-10 production by T cells An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. James Malone EFO:0001033 translation profiling assay An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|ELISA ELISA measuring epitope specific interleukin-15 production by T cells A cytometric bead array assay that detects interleukin-12 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-12 production by T cells in vitro design A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture. Person: Chris Stoeckert, Jie Zheng MO_347 in_vitro_design in vitro design RNAi profiling by array design A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team RNAi profiling by array design An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB lymphotoxin A/TNFb release|ELISA ELISA measuring epitope specific lymphotoxin A production by T cells A cytometric bead array assay that detects interleukin-5 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-5 production by T cells transcription profiling by array design A study design that identifies forms and abundance of transcripts in the genome using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_533 transcript_identification_design transcription profiling by array design A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|biological activity assay measuring epitope specific interleukin-15 production by T cells disease state design A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress. Person: Chris Stoeckert, Jie Zheng MO_902 disease_state_design disease state design wild type organism genotype information C57BL/6J wild type a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group wild type organism genotype information A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|biological activity assay measuring epitope specific interleukin-17 production by T cells A cytometric bead array assay that detects interleukin-17 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17 production by T cells A cytometric bead array assay that detects interleukin-10 production by T cells. IEDB IEDB IL-10 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-10 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells A flow cytometry assay that detects interleukin-5 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells A cytometric bead array assay that detects interleukin-2 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-2 production by T cells A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL3/MIP-1a release|ELISA ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|ICS intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression. James Malone EFO:0001030 RNAi profiling by array assay genotype information Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc. discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genotype information RNA stability design A study design that examines the stability and/or decay of RNA transcripts. Person: Chris Stoeckert, Jie Zheng MO_553 RNA_stability_design RNA stability design tiling microarray A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. Person: Helen Parkinson genome tiling array EFO_0002704: tiling array tiling microarray A T cell epitope specific cytokine production assay that detects IP-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|biological activity assay measuring epitope specific IP-10 production by T cells A flow cytometry assay that detects interleukin-13 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-13 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells species comparison design A study design that assays differences between distinct species. Person: Chris Stoeckert, Jie Zheng MO_675 species_design species comparison design A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|x-ray crystallography|angstroms X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex transcription profiling by RT-PCR design A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team transcription profiling by RT-PCR design epitope specific T cell enhancement of B cell mediated immune response A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific T cell enhancement of B cell mediated immune response An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|ELISA ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells epitope specific interleukin-21 production by T cells A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-21 production by T cells A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB T cell- APC binding|binding assay flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology. James Malone EFO:0002765 proteomic profiling by array assay A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|bioassay cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|ELISPOT ELISPOT assay measuring epitope specific granzyme B release by T cells microRNA profiling by array design A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team microRNA profiling by array design An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB tolerance|in vivo assay in vivo assay measuring T cell epitope specific tolerance induction A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells. IEDB IEDB CCL5/RANTES release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells A cytometric bead array assay that detects interleukin-4 production by T cells PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-4 production by T cells A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB lymphotoxin A/TNFb release|biological activity assay measuring epitope specific lymphotoxin A production by T cells organism development design A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. Person: Chris Stoeckert, Jie Zheng MO_892 development_or_differentiation_design organism development design family history design A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. Person: Chris Stoeckert, Jie Zheng MO_544 family_history_design family history design An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. IEDB IEDB CXCL9/MIG release|ELISA ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells transcription profiling identification objective A molecular feature identification objective that aims to characterize the abundance of transcripts Person: Chris Stoeckert, Jie Zheng Group: Penn Group transcription profiling identification objective A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology James Malone EFO:0002759 DNA methylation profiling by array assay A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL3/MIP-1a release|biological activity assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells epitope specific granulocyte colony stimulating factor production by T cells A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific granulocyte colony stimulating factor production by T cells An assay that analyses the microRNA component of the transcriptome using a microRNA array. James Malone EFO:0000753 microRNA profiling by array assay quality control testing design A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. Person: Chris Stoeckert, Jie Zheng MO_981 quality_control_testing_design quality control testing design clinical history design A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied. Person: Chris Stoeckert, Jie Zheng MO_832 clinical_history_design clinical history design A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|bioassay cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells A flow cytometry assay that detects interleukin-21 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|ELISA ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL4/MIP-1b release|biological activity assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|ELISA ELISA measuring epitope specific interleukin-21 production by T cells An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB type IV hypersensitivity (DTH)|in vivo skin test in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity A cytometric bead array assay that detects interleukin-13 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-13 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-13 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells epitope specific tumor necrosis factor superfamily cytokine production by T cells A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific tumor necrosis factor superfamily cytokine production by T cells allele information genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_58 Allele allele information A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|cytometric bead array cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells An enzyme-linked immunospot assay that detects interleukin-17 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-17 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells post-transcriptional modification design A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases Person: Chris Stoeckert, Jie Zheng MO_392 cellular_modification_design post-transcriptional modification design An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-8 release|ELISA ELISA measuring epitope specific interleukin-8 production by T cells A cytometric bead array assay that detects interleukin-6 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-6 production by T cells A transcription profiling assay that uses reverse transcription PCR (RT-PCR). Anna Farne EFO:0002943 transcription profiling by RT-PCR assay epitope specific chemokine (C-C motif) ligand 4 production by T cells A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific chemokine (C-C motif) ligand 4 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|biological activity assay measuring epitope specific interleukin-23 production by T cells genetic alteration information a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc. proposed and discussed on San Diego OBI workshop, March 2011 Group: OBI group Group: OBI group genetic alteration information cellular process design A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. Person: Chris Stoeckert, Jie Zheng MO_810 cellular_process_design cellular process design epitope specific RANTES production by T cells A process of RANTES production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific RANTES production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-10 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNF release|cytometric bead array cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells wild type allele information an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism. discussed on San Diego OBI workshop, March 2011 Person: Chris Stoeckert, Jie Zheng MO_605 genotype wild type allele information A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL4/MIP-1b release|ICS intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells epitope specific granzyme B production by T cells A process of granzyme B production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific granzyme B production by T cells epitope specific interleukin-8 production by T cells A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-8 production by T cells injury design A study design in which the response of an organism(s) to injury or damage is studied. Person: Chris Stoeckert, Jie Zheng MO_726 injury_design injury design A flow cytometry assay that detects interleukin-3 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells organism status comparison design A study design that compares samples from live and dead organisms. Person: Chris Stoeckert, Jie Zheng MO_841 organism_status_design organism status comparison design An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL4/MIP-1b release|ELISA ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells A cytometric bead array assay that detects interferon-gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|cytometric bead array cytometric bead array assay measuring epitope specific interferon-gamma production by T cells A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|biological activity assay measuring epitope specific interleukin-18 production by T cells epitope specific interleukin-23 production by T cells A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-23 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNF release|ICS intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells epitope specific monocyte chemotactic protein-1 production by T cells A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific monocyte chemotactic protein-1 production by T cells genotyping by array design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping by array design A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|biological activity assay measuring epitope specific interleukin-1 alpha production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|biological activity assay measuring epitope specific interferon-beta production by T cells A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|biological activity assay measuring epitope specific interleukin-12 production by T cells An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB cytotoxicity|in vivo assay in vivo assay measuring epitope specific T cell killing An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria. James Malone array CGH EFO:0000749 comparative genomic hybridization by array assay epitope specific cytotoxic T cell degranulation A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific cytotoxic T cell degranulation A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells stimulus or stress design A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc. Person: Chris Stoeckert, Jie Zheng MO_568 stimulus_or_stress_design stimulus or stress design A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB G-CSF release|cytometric bead array cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells protein and DNA interaction identification objective A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites. Person: Chris Stoeckert, Jie Zheng MO_933 binding_site_identification_design protein and DNA interaction identification objective epitope specific interleukin-22 production by T cells A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-22 production by T cells A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNF release|biological activity assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells protocol optimization design A study design where different protocols or protocol parameters are compared aims to find an optimized protocol Person: Chris Stoeckert, Jie Zheng MO_934 optimization_design protocol optimization design A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells. IEDB IEDB IL-2 release|reporter gene assay promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells ChIP-chip design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays. Person: Chris Stoeckert, Jie Zheng ChIP-on-chip design MO_933 binding_site_identification_design ChIP-chip design genetic characteristics information a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes. Person: Chris Stoeckert, Jie Zheng MO_66 IndividualGeneticCharacteristics MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid) genetic characteristics information A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL3/MIP-1a release|cytometric bead array cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|biological activity assay measuring epitope specific interleukin-3 production by T cells A T cell epitope dependent biological activity assay that detects T cell activation. IEDB IEDB activation|biological activity assay measuring epitope specific T cell activation imprinting design A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared. Person: Chris Stoeckert, Jie Zheng MO_914 imprinting_design imprinting design cell cycle design A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells. Person: Chris Stoeckert, Jie Zheng MO_822 cell_cycle_design cell cycle design translation profiling design A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team translation profiling design cell type comparison design A study design that compares cells of different type, for example different cell lines. Person: Chris Stoeckert, Jie Zheng MO_764 cell_type_comparison_design cell type comparison design A cytometric bead array assay that detects RANTES production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|cytometric bead array cytometric bead array assay measuring epitope specific RANTES production by T cells A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|bioassay cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|biological activity assay measuring epitope specific interferon-gamma production by T cells epitope specific interleukin-9 production by T cells A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-9 production by T cells An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|biological activity assay measuring epitope specific tumor necrosis factor alpha production by T cells ChIP-chip by tiling array design A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. Person: Chris Stoeckert, Jie Zheng Group: ArrayExpress production team ChIP-chip by tiling array design dose response design A study design that examines the relationship between the size of the administered dose and the extent of the response. Person: Chris Stoeckert, Jie Zheng MO_485 dose_response_design dose response design A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin ArrayExpress production team EFO:0002762 ChIP-chip by tiling array assay epitope specific helper T cell enhancement of T cell mediated immune response A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific helper T cell enhancement of T cell mediated immune response epitope specific interferon-beta production by T cells A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interferon-beta production by T cells organism part comparison design A study design that compares tissues, regions, organs within or between organisms Person: Chris Stoeckert, Jie Zheng MO_953 organism_part_comparison_design organism part comparison design A flow cytometry assay that detects epitope specific granzyme B release by T cells PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|intracellular staining intracellular material detection measuring epitope specific granzyme B release by T cells protein binding site identification design A study design that investigates protein binding sites on nucleic acids. Person: Chris Stoeckert, Jie Zheng MO_933 binding_site_identification_design protein binding site identification design sex comparison design A study design that assays differences associated with an organism's sex, gender or mating type. Person: Chris Stoeckert, Jie Zheng MO_575 sex_design sex comparison design transcription profiling by tiling array design A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. Person: Chris Stoeckert, Jie Zheng MO_507 tiling_path_design transcription profiling by tiling array design cell differentiation design A study design that assays events associated with cell development or differentiation. Person: Chris Stoeckert, Jie Zheng MO_892 development_or_differentiation_design cell differentiation design transcription profiling design A study design that identifies forms and abundance of transcripts in the genome. Person: Chris Stoeckert, Jie Zheng MO_533 transcript_identification_design transcription profiling design operon identification design A study design that identifies locations and members of operons in a genome. Person: Chris Stoeckert, Jie Zheng MO_772 operon_identification_design operon identification design A radio immuno assay that detects interferon-gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNg release|radio immuno assay (RIA) radio immuno assay measuring epitope specific interferon-gamma production by T cells DNA methylation profiling by high throughput sequencing design A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology. Person: Chris Stoeckert, Jie Zheng GROUP: ArrayExpress production team DNA methylation profiling by high throughput sequencing design A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|biological activity assay measuring epitope specific granzyme B release by T cells A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL9/MIG release|ICS intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|ELISA ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells epitope specific chemokine (C-X-C motif) ligand 9 production by T cells A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific chemokine (C-X-C motif) ligand 9 production by T cells all pairs design A study design in which all specimens are compared to every other specimen. Person: Chris Stoeckert, Jie Zheng MO_565 all_pairs all pairs design A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology. Person: Chris Stoeckert, Jie Zheng, Dan Berrios Group: ArrayExpress production team https://github.com/obi-ontology/obi/issues/854 proteomic profiling by array design q-value PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)" A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level. PERS:Philippe Rocca-Serra FDR adjusted p-value Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html q-value genotyping design A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs. Person: Chris Stoeckert, Jie Zheng MO_560 genotyping_design genotyping design A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-2 release|biological activity assay measuring epitope specific interleukin-2 production by T cells epitope specific interleukin-15 production by T cells A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-15 production by T cells epitope specific macrophage inflammatory protein-1 gamma production by T cells A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific macrophage inflammatory protein-1 gamma production by T cells individual genetic characteristics comparison design A study design where genotype, haplotype, or other individual genetic characteristics are compared. Person: Chris Stoeckert, Jie Zheng MO_527 individual_genetic_characteristics_design individual genetic characteristics comparison design A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1b release|biological activity assay measuring epitope specific interleukin-1 beta production by T cells A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-4 release|biological activity assay measuring epitope specific interleukin-4 production by T cells A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-6 release|biological activity assay measuring epitope specific interleukin-6 production by T cells A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFa release|bioassay cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells A flow cytometry assay that detects lymphotoxin A production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB lymphotoxin A/TNFb release|ICS intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells pathogenicity design A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed. Person: Chris Stoeckert, Jie Zheng MO_807 pathogenicity_design pathogenicity design An enzyme-linked immunospot assay that detects interleukin-5 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-5 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-5 production by T cells A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|biological activity assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells A cytometric bead array assay that detects interleukin-8 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-8 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-8 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL9/MIG release|biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells genetic modification design A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out. Person: Chris Stoeckert, Jie Zheng MO_447 genetic_modification_design genetic modification design An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB granzyme B release|ELISA ELISA measuring epitope specific granzyme B release by T cells epitope specific IP-10 production by T cells A process of IP-10 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-04-01; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific IP-10 production by T cells A transcription profiling assay that uses array technology. James Malone RNA profiling by array assay EFO:0002768 https://sourceforge.net/p/obi/obi-terms/757/ transcription profiling by array assay strain comparison design A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. Person: Chris Stoeckert, Jie Zheng MO_462 strain_or_line_design strain comparison design A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|biological activity assay measuring epitope specific monocyte chemotactic protein-1 production by T cells A flow cytometry assay that detects interleukin-12 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. IEDB IEDB disease exacerbation|in vivo assay in vivo assay measuring T cell epitope specific disease exacerbation cell specimen A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture. Discussed on obi call Jan 23, 2017. To improve cell specimen that include single cell specimen. Details see tracker: https://sourceforge.net/p/obi/obi-terms/828 PERSON: Chris Stoeckert, Jie Zheng, Alexander Diehl MO_612 cell cell specimen A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB ligand presentation|T cell recognition monospecific T cell recognition assay measuring MHC ligand processing and presentation epitope specific interleukin-17F production by T cells A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-06-27; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mapping: e_specific_mappings.owl epitope specific interleukin-17F production by T cells T cell epitope specific immune intervention Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide An epitope specific immune intervention in which the induced response targets a T cell epitope PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters IEDB T cell epitope specific immune intervention specimen with known storage state A specimen for which it is known whether it has been subjected to storage of a specified type. PERSON: Chris Stoeckert, Jie Zheng MO_95 BiosourceType specimen with known storage state An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden. IEDB IEDB tumor burden after challenge|in vivo assay in vivo assay measuring T cell epitope specific protection after tumor burden challenge lowess group transformation A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed. Person: Elisabetta Manduchi MO_861 lowess_group_normalization lowess group transformation An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden. IEDB IEDB pathogen burden after challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden Using a commercial library of phages that produce random peptide sequences to infect E coli cells, and screening them for binding to a selecting antibody of unknown specificity. By iteratively using phages from selected E coli cells and repeating this process, phages encoding high affinity peptides for the antibody are selected, sequenced, and thereby the specificity of the antibody is elucidated. A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner. IEDB IEDB phage display binding assay lowess transformation A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria. Person: Elisabetta Manduchi MO_720 lowess_normalization lowess transformation A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands IEDB IEDB ligand presentation|mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). PERSON: Chris Stoeckert, Jie Zheng tissue specimen MO_954 organism_part specimen from organism phage display library panning Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind. Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection. Jason Greenbaum, Randi Vita, Bjoern Peters IEDB, http://en.wikipedia.org/wiki/Phage_display phage display library panning lowess global transformation A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample. Person: Elisabetta Manduchi MO_692 lowess_global_normalization lowess global transformation A flow cytometry assay that detects transforming growth factor-beta production by T cells. IEDB IEDB TGFb release|ICS intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells cell collecting A planned process that collects cells from culture. PERSON: Chris Stoeckert, Jie Zheng MO_982 harvest cell collecting A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. IEDB IEDB in vivo activity|biological activity assay measuring T cell epitope specific in vivo activity purified MHC molecule preparation HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody. A mixture containing MHC molecules that was purified to remove non-MHC molecular entities. BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general. Bjoern Peters purified MHC molecule preparation disposition to be bound by an MHC protein complex Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex. PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters MHC ligand disposition IEDB disposition to be bound by an MHC protein complex B cell epitope specific immune intervention Injecting a mouse with recombinant antibody targeting an anthrax epitope An epitope specific immune intervention in which the induced response targets a B cell epitope PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters IEDB B cell epitope specific immune intervention An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response IEDB tolerance induction IEDB epitope tolerance induction experiment A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC. IEDB IEDB ligand presentation|cellular MHC/mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB GM-CSF release|cytometric bead array cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells A binding assay that uses radioactivity detection as an indicator of binding. Bjoern Peters Randi Vita IEDB binding assay using radioactivity detection An in vivo assay measuring T cell epitope specific protection from other challenge using survival. IEDB IEDB survival from challenge|in vivo assay in vivo assay measuring T cell epitope specific protection based on survival A cell bound MHC binding assay that uses a T cell epitope recognition assay. IEDB IEDB qualitative binding|cellular MHC/T cell inhibition cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition linear amplification An example is the use of the T7 promoter for amplification by transcribing many RNA copies. An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. PERSON: Chris Stoeckert, Jie Zheng MO_997 linear_amplification linear amplification A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function. IEDB IEDB helper response|in vivo assay in vivo assay measuring epitope specific T cell helper activity A flow cytometry assay that detects interleukin-22 production by T cells. IEDB IEDB IL-22 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells. IEDB IEDB perforin release|biological activity assay measuring epitope specific perforin release by T cells atmosphere A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism. PERSON: Chris Stoeckert, Jie Zheng MO_219 atmosphere atmosphere A binding assay that uses fluorescence detection as an indicator of binding. Bjoern Peters Randi Vita IEDB binding assay using fluorescence detection A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB ligand presentation|coelution coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for. An assay in which a material's fluorescence is determined. IEDB IEDB fluorescence detection assay epitope specific perforin production by T cells The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope. Should be linked to a GO process, which will be requested by IEDB team. Along with granzyme B production, should be tied to T cell degranulation PERSON: Bjoern Peters, Randi Vita epitope specific perforin production by T cells MHC protein complex binding to ligand The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex. The process in which a ligand binds to an MHC molecule to form a stable complex. 6/13/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. PERSON: Bjoern Peters; Randi Vita IEDB MHC protein complex binding to ligand dissection A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. PERSON: Chris Stoeckert, Jie Zheng EFO_0003856 dissection MO_374 dissect dissection purification A planned process 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: Chris Stoeckert, Jie Zheng MO_406 purify purification specimen with pre- or post-mortem status A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism. organizational term, used in description of specimen that is created from known pre- or post-mortem status PERSON: Chris Stoeckert, Jie Zheng MO_84 OrganismStatus specimen with pre- or post-mortem status An efficacy of T cell epitope intervention experiment that detects a decrease in disease. IEDB IEDB decreased disease|in vivo assay in vivo assay measuring T cell epitope specific treatment of disease sampling time measurement datum A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point. Person: Chris Stoeckert time point MO_738 timepoint sampling time measurement datum A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB ligand presentation|Edman degradation Edman degradation assay measuring MHC ligand processing and presentation A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC. IEDB IEDB ligand presentation|secreted MHC/mass spectrometry mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC disposition to be a product of antigen processing and presentation The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER. A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell. IEDB IEDB disposition to be a product of antigen processing and presentation A cytometric bead array assay that detects interleukin-17A production by T cells. IEDB IEDB IL-17A release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17A production by T cells A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|purified MHC/competitive/radioactivity radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex minimal inhibitory concentration A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound. Created following request by Albert Goldfain PERSON:Bjoern Peters Bjoern Peters, coordinated with Albert Goldfain minimal inhibitory concentration material maintenance service model organism colony maintanance A material processing service in which a service provider makes physical modifications to a specified input material, such that at least one of the specified outputs of this process is a modified version of a specified input material. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. material maintenance service A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|lysate MHC/direct/fluorescence fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells. IEDB IEDB G-CSF release|ELISA ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells sequence assembly algorithm An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Assembly Algorithm NIAID GSCID-BRC sequence assembly algorithm A cytometric bead array assay that detects interleukin-17F production by T cells. IEDB IEDB IL-17F release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-17F production by T cells A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand. IEDB IEDB association constant KA|cellular MHC/direct/fluorescence|1/M fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex PDB file The file found in the pdb with the identifier 3pe4 http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=3pe4 A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned. PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum PDB file epitope specific interleukin-17A production by T cells A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl epitope specific interleukin-17A production by T cells support service An help desk for an instrument or a software. A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON; Carlo Torniai support service material service A service performing DNA sequencing, a service preforming cell analysis. A service performing cell line immortalization A service which has a material entity as specified input and/or specified output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai material service data analysis service Statistaical analysis service, data visualization service A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush data analysis service data service Data analysis service such statistical abalysis or storage service such data backup. A service that has some information content entity as input and output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai Information content entity was used as specified input and output since it was more appropriate then data item or dataset. data service A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. IEDB IEDB half life|purified MHC/direct/fluorescence|min fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex A cytometric bead array assay that detects interleukin-9 production by T cells. IEDB IEDB IL-9 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-9 production by T cells data storage service A service offering data backup A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush data storage service A fluorescence detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. IEDB IEDB qualitative binding|purified MHC/competitive/fluorescence fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex epitope specific interleukin-7 production by T cells A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl epitope specific interleukin-7 production by T cells equilibrium dissociation constant (KD) KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate) PERSON: Bjoern Peters, Randi Vita IEDB equilibrium dissociation constant (KD) A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|purified MHC/competitive/fluorescence|nM fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex training service A service that offers training for a specific instrument or technique. A course to learn how to use a microscope A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush training service A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. IEDB IEDB dissociation constant KD|cellular MHC/competitive/fluorescence|nM fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex Using proliferation of a T cell line specific for SIINFEKL in response to material eluted from a cell as evidence that SIINFEKL was presented by MHC on that cell. An assay that identifies an MHC ligand using a T cell response assay as a readout PERSON: Randi Vita, Bjoern Peters IEDB T cell recognition obsolete T cell recognition of eluted MHC ligand assay true A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex. IEDB IEDB on rate|purified MHC/direct/fluorescence|nM^-1s^-1 fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex A detection of specific nucleic acid polymers with complementary probes that detects interleukin-13 production by T cells. IEDB IEDB IL-13 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect direct binding of a purified-MHC molecule with a ligand and provides EC50 values determined under assay conditions where the EC50 approximates a KD value. IEDB IEDB dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50 A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-lysate-MHC due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|lysate MHC/competitive/radioactivity|nM radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells. IEDB IEDB CCL3/MIP-1a release|ICS intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells comparative phenotypic assessment Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference Philly workshop 2011 Philly workshop 2011 6/1/2012: We will utilize 'comparative qualities' once they are available in BFO2 comparative phenotypic assessment material analysis service Services performing DNA sequencing or Cell Analysis A service in which a service consumer provides some input material and a service provider performs some analysis of this material to generate data that is returned to the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material analysis service equilibrium association constant (KA) KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens. A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate) PERSON: Bjoern Peters, Randi Vita IEDB equilibrium association constant (KA) A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|cellular MHC/competitive/radioactivity|nM radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex A qualitative binding assay that detects the binding of a cell-bound-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|cellular MHC assay measuring binding of a cell-bound-MHC:ligand complex access service A service that provides acess to a mass spectrometer. A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service. Need to come up wiht a proper logical defintion. One option woudl be to dfine provides_access_to property as shortcut of participants in a process. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush access service A flow cytometry assay that detects tumor necrosis factor (ligand) superfamily member 11 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB TNFSF11/RANKL release|ICS intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells A MHC:ligand binding assay that measures a binding constant. IEDB IEDB binding constant|binding assay assay measuring a binding constant of a MHC:ligand complex rate measurement datum The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time. A scalar measurement datum that represents the number of events occuring over a time interval PERSON: Bjoern Peters, Randi Vita IEDB rate measurement datum A qualitative binding assay that detects the binding of a purified-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|purified MHC assay measuring binding of a purified-MHC:ligand complex A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|lysate MHC/direct/radioactivity radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex material storage service A service that offers liquid nitrogen stroage. A storage service in which a service consumer provides some material as input which a service provider stores and returns as output. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush material storage service A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. IEDB IEDB half life|cellular MHC/direct/radioactivity|min radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half life|cellular MHC/direct/fluorescence|min fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant. PERSON: Bjoern Peters IEDB obsolete cell lysate MHC binding constant determination assay true A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand. IEDB IEDB half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex A flow cytometry assay that detects interleukin-17F production by T cells. IEDB IEDB IL-17F release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells material processing service A service for cell line creation. A service providing cel line immortalization. A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai material processing service A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. IEDB IEDB dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half life|lysate MHC/direct/radioactivity|min radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex 50% dissociation of binding temperature (Tm) Preparing a complex of a purified HLA-A*02:01 bound to a specific peptide ligand, varying the temperature while detecting the fraction of bound complexes with a complex conformation specific antibody, and interpolating the temperature at which 50% of complexes are dissociated. A quantitative binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound. PERSON: Bjoern Peters, Randi Vita melting temperature (Tm) IEDB 50% dissociation of binding temperature (Tm) A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|lysate MHC/direct/radioactivity|1/s radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a purified-MHC molecule with a ligand. IEDB IEDB off rate|purified MHC/direct/fluorescence|1/s fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|biological activity assay measuring epitope specific vascular endothelial growth factor production by T cells equilibrium dissociation constant (KD) approximated by IC50 A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor. PERSON: Bjoern Peters, Randi Vita http://dx.doi.org/10.1016/0006-2952(73)90196-2 equilibrium dissociation constant (KD) approximated by IC50 An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant. PERSON: Bjoern Peters IEDB obsolete cell bound MHC binding constant determination assay true DNA sequence data The part of a FASTA file that contains the letters ACTGGGAA A sequence data item that is about the primary structure of DNA OBI call; Bjoern Peters OBI call; Melanie Courtout 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. DNA sequence data competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) cell lysate MHC competitive binding using radioactivity obsolete cell lysate MHC competitive binding assay using radioactivity detection true assigning gene property based on phenotypic assessment Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result. Philly workshop 2011 Philly workshop 2011 assigning gene property based on phenotypic assessment An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant. PERSON: Bjoern Peters IEDB obsolete purified MHC binding constant determination assay true A cytometric bead array assay that detects interleukin-22 production by T cells. IEDB IEDB IL-22 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells An enzyme-linked immunosorbent assay that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|ELISA ELISA measuring epitope specific vascular endothelial growth factor production by T cells A qualitative binding assay that detects the binding of a cell-lysate-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|lysate MHC assay measuring binding of a cell-lysate-MHC:ligand complex material transport service A service for chemical disposal A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Carlo Torniai material transport service equilibrium dissociation constant (KD) approximated by EC50 A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand. PERSON: Bjoern Peters, Randi Vita Assay Development: Fundamentals and Practices, By Ge Wu, page 74 equilibrium dissociation constant (KD) approximated by EC50 direct binding assay measuring MHC ligand binding using MHC derived from a cell PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) cell bound MHC direct binding obsolete cell bound MHC direct binding assay true half life of binding datum The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate. A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association. PERSON: Bjoern Peters, Randi Vita IEDB half life of binding datum A phage display binding assay that detects direct binding of a purified-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|purified MHC/direct/phage display phage display binding assay measuring binding of a purified-MHC:ligand complex A cytometric bead array assay that detects interleukin-7 production by T cells. IEDB IEDB IL-7 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-7 production by T cells A radioactivity detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half life|purified MHC/direct/radioactivity|min radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells. IEDB IEDB IL-7 release|biological activity assay measuring epitope specific interleukin-7 production by T cells binding A peptide binding to an MHC molecule to form a complex. The process of material entities forming complexes. 9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. PERSON: Bjoern Peters, Randi Vita IEDB binding A flow cytometry assay that detects interleukin-17A production by T cells. IEDB IEDB IL-17A release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells A fluorescence detection assay that detects direct binding of a purified-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|purified MHC/direct/fluorescence fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex Detecting the binding of a fluorescently labeled antibody to a peptide bound to the bottom of an ELISA plate, by incubating the antibody in the well, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody._ A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand. Bjoern Peters Randi Vita IEDB direct binding assay A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a purified-MHC molecule with a ligand. IEDB IEDB half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex Detecting the inhibition of binding of a fluorescently labeled antibody to its known protein ligand bound to the bottom of an ELISA plate, by incubating the antibody in the presence of a peptide of interest, adding it to the plate, washing the plate, and detecing fluorescence which is a proxy for the presence of the bound antibody. Reduction in binding due to the presence of the peptide indicates that the antibody binds the peptide._ A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material. IEDB IEDB competitive inhibition of binding assay A fluorescence detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|cellular MHC/competitive/fluorescence fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a MHC:ligand complex. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|x-ray crystallography|angstroms X-ray crystallography assay determining the 3D structure of a MHC:ligand complex PDB file chain The 'D' chain in the PDB file 2BSE identifies the heavy chain of the antibody in the protein:antibody complex A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities. PERSON: Bjoern Peters, Dorjee Tamang, Jason Greenbaum IEDB PDB file chain A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding. IEDB IEDB half maximal inhibitory concentration (IC50)|cellular MHC/T cell inhibition|nM cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition data maintenance service A database management service, a web hosting service. A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance. PERSON: Carlo Torniai PERSON: Matthew Brush PERSON: Matthew Brush data maintenance service A radioactivity detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation. IEDB IEDB qualitative binding|cellular MHC/competitive/radioactivity radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells. IEDB IEDB G-CSF release|biological activity assay measuring epitope specific granulocyte colony stimulating factor production by T cells A cytometric bead array assay that detects interleukin-21 production by T cells. IEDB IEDB IL-21 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells A radioactivity detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|cellular MHC/direct/radioactivity radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex binding off rate measurement datum (koff) A rate measurement datum of how quickly bound complexes disassociate PERSON: Bjoern Peters, Randi Vita IEDB binding off rate measurement datum (koff) A fluorescence detection assay that measures the 50% dissociation of binding temperature of a purified-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 50% dissociation temperature|purified MHC/direct/fluorescence|°C fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex binding on rate measurement datum (kon) A rate measurement datum of how quickly bound complexes form PERSON: Bjoern Peters, Randi Vita IEDB binding on rate measurement datum (kon) A fluorescence detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|cellular MHC/direct/fluorescence fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production. IEDB IEDB TNFSF11/RANKL release|biological activity assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand. IEDB IEDB qualitative binding|purified MHC/direct/radioactivity radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex A flow cytometry assay that detects interleukin-8 production by T cells. IEDB IEDB IL-8 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells A cytometric bead array assay that detects interleukin-23 production by T cells. IEDB IEDB IL-23 release|cytometric bead array cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-23 production by T cells direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) purified MHC direct binding obsolete purified MHC direct binding assay true epitope specific vascular endothelial growth factor production by T cells A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-11-10; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: assay_mappings.owl epitope specific vascular endothelial growth factor production by T cells A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex GenBank ID A CRID symbol uniquely indentifies the submitted GeneBank sequence record. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group GenBank Record ID NIAID GSCID-BRC GenBank ID investigation description A textual entity that describes an investigation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group study description project description NIAID GSCID-BRC investigation description specimen identifier A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. Person: Chris Stoeckert, Jie Zheng specimen ID NIAID GSCID-BRC metadata working group Specimen ID NIAID GSCID-BRC specimen identifier 1 PubMed ID A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information. Edits was made on Aug 24, 2016 based on OBI dev call, details see tracker: https://sourceforge.net/p/obi/obi-terms/819/ Person: Chris Stoeckert, Jie Zheng PMID PubMed Identifier Website: http://en.wikipedia.org/wiki/Wikipedia:PMID Publication Citation NIAID GSCID-BRC PubMed ID average depth of sequence coverage An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Depth of Coverage - Average NIAID GSCID-BRC average depth of sequence coverage specimen collection time measurement datum A time measurement datum that is the measure of the time when the specimens are collected. Person: Chris Stoeckert, Jie Zheng collection date NIAID GSCID-BRC metadata working group Specimen Collection Date NIAID GSCID-BRC specimen collection time measurement datum latitude coordinate measurement datum A measurement datum that is the measure of the latitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng latitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Latitude NIAID GSCID-BRC latitude coordinate measurement datum longitude coordinate measurement datum A measurement datum that is the measure of the longitude coordinate of a site. Person: Chris Stoeckert, Jie Zheng longitude NIAID GSCID-BRC metadata working group Specimen Collection Location - Longitude NIAID GSCID-BRC longitude coordinate measurement datum investigation title A textual entity that denotes an investigation. Person:Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group study title project title NIAID GSCID-BRC investigation title organism identification objective A biological feature identification objective to identify the organism species in a specimen. Person: Chris Stoeckert, Jie Zheng Penn Group organism species detection objective An organism detection assay that identifies the organism species in a specimen. Chris Stoeckert Jie Zheng organism identification assay NIAID GSCID-BRC metadata working group organism species detection assay sequence annotation algorithm An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Annotation Algorithm NIAID GSCID-BRC sequence annotation algorithm Bioinformatics Resource Center An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them. Person: Chris Stoeckert, Jie Zheng BRC Website: http://en.wikipedia.org/wiki/Bioinformatics_Resource_Centers NIAID GSCID-BRC Bioinformatics Resource Center country name A textual entity that denotes a geographic location that is a site or part of a site that is identified as a country in the political geography. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Website: http://en.wikipedia.org/wiki/Country Specimen Collection Location - Country NIAID GSCID-BRC country name investigation identifier A CRID symbol used to identify an investigation. Person: Chris Stoeckert, Jie Zhneg NIAID GSCID-BRC metadata working group project ID NIAID GSCID-BRC investigation identifier grant identifier A CRID symbol used to identify a grant. Person: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group grant ID NIAID GSCID-BRC grant identifier Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column. An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material. IEDB IEDB analytical chromatography Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure. An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material. IEDB IEDB electron microscopy imaging assay Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye. A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity. IEDB IEDB immuno staining assay purified material A mixture of peptide molecules that has been run through an HPLC column to remove 65 A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component GROUP: OBI call OBI conference call purified material A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (delta H) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell ._ A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy. IEDB IEDB calorimetric binding assay The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844). A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope). IEDB IEDB antibody binding detection by fluorescence quenching grant A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role. Discussed on Feb 13, 2012 dev call. Details see the tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 Group: OBI OBI AR: Grant isn't a plan specification, it has a part which is a plan specification. See tracker: https://sourceforge.net/tracker/?func=detail&aid=3483338&group_id=177891&atid=886178 grant A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|inhibition by antigen (~ IC50)|nM antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 A B cell epitope specific activation of additional immune response assay that detects histamine release in vitro. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB histamine release|biological activity assay measuring epitope specific Ig-mediated histamine release A B cell epitope dependent biological activity determination assay that detects antigen activation. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB antigen activation|biological activity assay measuring epitope specific immunoglobulin-mediated antigen activation A B cell epitope specific activation of additional immune response assay that detects complement-dependent cytotoxicity in vitro . PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB complement-dependent cytotoxicity|biological activity assay measuring epitope specific complement-dependent cytotoxicity A B cell epitope specific activation of additional immune response assay that detects antibody-dependent cellular cytotoxicity in vitro. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB antibody-dependent cellular cytotoxicity|biological activity assay measuring epitope specific antibody-dependent cellular cytotoxicity A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB neutralization |biological activity assay measuring epitope specific immunoglobulin-mediated neutralization A B cell epitope specific activation of additional immune response assay that detects opsonization in vitro . PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB opsonization|biological activity assay measuring epitope specific opsonization A calorimetric binding assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|calorimetry calorimetry assay measuring binding of a B cell epitope:antibody complex An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|electron microscopy electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex A nuclear magnetic resonance 3D molecular structure determination assay that characterizes the 3-dimensional structure of a B cell epitope:antibody complex. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|nuclear magnetic resonance (NMR) NMR assay determining the 3D structure of a B cell epitope:antibody complex A cross-blocking assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|cross blocking cross blocking assay measuring binding of a B cell epitope:antibody complex A radio immuno assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|radio immuno assay (RIA) RIA measuring binding of a B cell epitope:antibody complex An immunoblot assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|western blot immunoblot assay measuring binding of a B cell epitope:antibody complex A surface plasmon resonance binding assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|surface plasmon resonance (SPR) plasmon resonance assay measuring binding of a B cell epitope:antibody complex An immuno staining assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|immuno staining immuno staining assay measuring binding of a B cell epitope:antibody complex An immunoprecipitation assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|immunoprecipitation immunoprecipitation assay measuring binding of a B cell epitope:antibody complex A mass spectrometry assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|mass spectrometry mass spectrometry assay measuring binding of a B cell epitope:antibody complex A phage display binding assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|phage display phage display assay measuring binding of a B cell epitope:antibody complex An electron microscopy imaging assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|electron microscopy electron microscopy assay measuring binding of a B cell epitope:antibody complex An enzyme-linked immunosorbent assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|ELISA ELISA measuring binding of a B cell epitope:antibody complex An enzyme-linked immunospot assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|ELISPOT ELISPOT assay measuring binding of a B cell epitope:antibody complex A flow cytometry assay that detects the binding of an antigen with an antibody. IEDB IEDB qualitative binding|flow cytometry flow cytometry assay measuring binding of a B cell epitope:antibody complex A flow cytometry assay that detects epitope specific granzyme A release by T cells. IEDB IEDB granzyme A release|intracellular staining intracellular material detection assay measuring epitope specific granzyme A release by T cells An analytical chromatography assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|chromatography chromatography assay measuring binding of a B cell epitope:antibody complex A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|nuclear magnetic resonance (NMR) NMR assay measuring binding of a B cell epitope:antibody complex An enzyme-linked immunosorbent assay that detects epitope specific granulysin release by T cells. IEDB IEDB granulysin release|ELISA ELISA measuring epitope specific granulysin release by T cells A flow cytometry assay that detects epitope specific granulysin release by T cells. IEDB IEDB granulysin release|intracellular staining intracellular material detection assay measuring epitope specific granulysin release by T cells A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a cell-bound-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|cellular MHC/direct/fluorescence|1/s fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex A fluorescence detection assay that measures binding on rate (kon) to detect direct binding of a cell-bound-MHC molecule with a ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB on rate|cellular MHC/direct/fluorescence|nM^-1s^-1 fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD (~IC50)|purified MHC/competitive/fluorescence|nM fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 Split-ubiquitin two-hybrid assay to analyze protein-protein interactions at the endosome: application to Saccharomyces cerevisiae Bro1 interacting with ESCRT complexes, the Doa4 ubiquitin hydrolase, and the Rsp5 ubiquitin ligase. PMID:17513562 A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. Marcus Chibucos Philippe Rocca-Serra url:https://en.wikipedia.org/wiki/Two-hybrid_screening split-ubiquitin assay Studying protein-protein interactions via blot overlay or Far Western blot. PMID:15064457 An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay. Marcus Chibucos Philippe Rocca-Serra PMID:18079728 far-western blot assay Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay. PMID:11518275 An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest. Marcus Chibucos Philippe Rocca-Serra RNAse protection assay RPA PMID:16491611 RNA protection assay Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein. PMID:21918373 An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid. Marcus Chibucos Philippe Rocca-Serra EMSA band shift assay gel mobility shift assay gel retardation assay gel shift assay PMID:6269071 electrophoretic mobility shift assay An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells. Marcus Chibucos Philippe Rocca-Serra PMID:17430206 gene knock-down assay Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan._PMID:20543846 A transcription profiling by RNA sequencing assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE). Marcus Chibucos Michelle Giglio Philippe Rocca-Serra Sebastian Duesing nano-CAGE PMID:20543846 nano-cap analysis of gene expression assay 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. PMID:22362160 A transcription profiling by RNA sequencing assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome Marcus Chibucos Michelle Giglio Philippe Rocca-Serra Sebastian Duesing CAGE PMID:14663149 cap analysis of gene expression assay An enzyme-linked immunosorbent assay that detects interleukin-17A production by T cells. IEDB IEDB IL-17A release|ELISA ELISA measuring epitope specific interleukin-17A production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-7 production by T cells. IEDB IEDB IL-7 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells epitope specific granulysin production by T cells A process of granulysin production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific granulysin production by T cells epitope specific granzyme A production by T cells A process of granzyme A production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2011-6-24; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific granzyme A production by T cells Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system. PMID:10627486 An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay. Marcus Chibucos Philippe Rocca-Serra Y2H url:https://en.wikipedia.org/wiki/Two-hybrid_screening yeast 2-hybrid assay The Sos-recruitment system as a tool to analyze cellular localization of plant proteins: membrane localization of Arabidopsis thaliana PEPINO/PASTICCINO2. PMID:20300944 A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using the Sos recruitment system, a kind of yeast 2 hybrid system. Marcus Chibucos Philippe Rocca-Serra SRS PMID:9154808 Sos-recruitment assay Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. PMID:22037702 An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain. Marcus Chibucos Philippe Rocca-Serra Y1H PMID:22218861 yeast one-hybrid assay A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. PMID:18332042 An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence Marcus Chibucos Philippe Rocca-Serra B1H url:http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system bacterial one-hybrid assay Duplication of intrachromosomal insertion segments 4q32__�q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization. PMID:22384449 An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity Marcus Chibucos Philippe Rocca-Serra https://github.com/obi-ontology/obi/issues/788| chromosome organization assay by fluorescence in-situ hybridization Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID:18219662 An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. Marcus Chibucos Philippe Rocca-Serra MSP PMID:8790415 methylation-specific polymerase chain reaction assay Analysis of DNA methylation by amplification of intermethylated sites (AIMS). PMID:18987810 An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences. Marcus Chibucos Philippe Rocca-Serra AIMS assay intermethylated site amplification PMID:18987810 amplification of intermethylated sites assay Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system. PMID:22639265 An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization. Marcus Chibucos Philippe Rocca-Serra ISH in situ hybridization PMID:9021518 in-situ hybridization assay contact representative role A role inhering in a person who represents an institution, organization, or service provider and realized when communication is directed at them about the entity they represent. Discussed on May 7, 2012 dev call propose:contact role, type of organization role, and create shortcut relation between 'organization role' and 'organization' ? Whether it works for communicating author in manuscript or not? Tracker: https://sourceforge.net/tracker/?func=detail&aid=3512891&group_id=177891&atid=886178 Person: Chris Stoeckert NIAID GSCID-BRC contact representative role An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041). Marcus Chibucos Philippe Rocca-Serra cytochalasin-induced inhibition of actin polymerization assay molecular function identification objective is an objective specification which aims to discover molecular function realized by a molecular entity PERSON:Philippe Rocca-Serra OBI group molecular function identification objective cellular structure feature identification objective is an objective specification which aims to discover cellular structure properties PERSON:Philippe Rocca-Serra OBI group cellular structure feature identification objective An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of fertility. PERSON:Randi Vita, James Overton, Bjoern Peters IEDB protection from fertility|in vivo assay in vivo assay measuring B cell epitope specific protection from fertility An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB tolerance|in vivo assay in vivo assay measuring B cell epitope specific tolerance induction An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB hypersensitivity|in vivo assay in vivo assay measuring B cell epitope specific induction of hypersensitivity A B cell epitope specific activation of additional immune response assay that detects agglutination in vitro. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB agglutination|biological activity assay measuring epitope specific immune complex formation An in vivo assay measuring B cell epitope specific protection from other challenge using survival. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB survival from challenge|in vivo assay in vivo assay measuring B cell epitope specific protection based on survival An efficacy of B cell epitope intervention experiment that detects a decrease in disease. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB decreased disease|in vivo assay in vivo assay measuring B cell epitope specific treatment of disease A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB in vivo activity|biological activity assay measuring B cell epitope specific in vivo activity Testing two antibodies that bind the HBV core protein for the ability of one antibody pre-incubated with the protein in solution to inhibit binding to the other antibody which is plate-bound in an ELISA format. A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites. IEDB antibody inhibition of antibody binding IEDB antibody cross-blocking assay Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum. An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies. IEDB IEDB immunoprecipitation assay A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|inhibition by antigen antigen inhibition assay measuring binding of a B cell epitope:antibody complex immunoglobulin binding to epitope Binding of the LA5 antibody to a discontinuous set of amino acid residues on the surface of the D8 protein of Vaccinia virus. a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). PERSON: Bjoern Peters, Randi Vita IEDB immunoglobulin binding to epitope An assay that detects the binding of an antigen with an antibody, and produces a qualitative measurement of the binding as an output. IEDB IEDB qualitative binding|binding assay assay measuring qualitative binding of a B cell epitope:antibody complex A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity. IEDB IEDB secondary in vitro activity|biological activity assay measuring epitope specific activation of additional immune response in vitro A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen. IEDB IEDB antibody activity inhibition|biological activity assay measuring epitope specific antigen inhibition of antibody activity A B cell epitope assay that measures the immune response process resulting from the binding of an antibody receptor to epitope or recognition of the epitope. IEDB IEDB biological activity|any method assay measuring biological activity resulting from B cell epitope:antibody binding immunoglobulin mediated histamine release The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins. 4/26/12, BP: We want to import this from GO, which currently only has IgE mediated histamine release. We have requested the term, but need to use this as a placeholder in the meanwhile. PERSON: Bjoern Peters, Randi Vita IEDB immunoglobulin mediated histamine release A B cell epitope binding constant determination assay that measures the dissociation constant KD. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|binding assay|nM assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB binding constant|binding assay assay measuring a binding constant of a B cell epitope:antibody complex An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB protection from challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from challenge An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB disease exacerbation|in vivo assay in vivo assay measuring B cell epitope specific disease exacerbation A direct binding assay using a assay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) direct binding assay obsolete B cell epitope direct binding assay true B cell epitope specific opsonization opsonization resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific opsonization B cell epitope specific immunoglobulin-mediated neutralization immunoglobulin-mediated neutralization resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific immunoglobulin-mediated neutralization A competitive inhibition of binding assay using a assay PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) competitive binding assay obsolete B cell epitope competitive binding assay true B cell epitope specific complement-dependent cytotoxicity complement-dependent cytotoxicity resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific complement-dependent cytotoxicity B cell epitope specific antibody-dependent cellular cytotoxicity antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific antibody-dependent cellular cytotoxicity A B cell epitope binding constant determination assay that measures the on rate. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB on rate|binding assay|M^-1s^-1 assay measuring the on rate [kon] of a B cell epitope:antibody complex A B cell epitope binding constant determination assay that measures the association constant KA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|binding assay|1/nM assay measuring the association constant [KA] of a B cell epitope:antibody complex B cell epitope specific immune complex formation immune complex formation resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific immune complex formation A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of an antigen:antobody complex. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|any method 3D molecular structure determination assay of an antigen:antibody complex B cell epitope specific hypersensitivity hypersensitivity resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific hypersensitivity A B cell epitope binding constant determination assay that measures the off rate. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|binding assay|1/s assay measuring the off rate [koff] of a B cell epitope:antibody complex A viral hemagglutination inhibition assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding| hemagglutination inhibition viral hemagglutination inhibition assay measuring binding of a B cell epitope:antibody complex B cell epitope specific histamine secretion mediated by immunoglobulin histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-05-03; Spreadsheet: BcellAssays.xls; Worksheet: Especific template; Mapping: ebcell_specific_mappings.owl B cell epitope specific histamine secretion mediated by immunoglobulin A fluorescence quenching assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|quenching quenching assay measuring binding of a B cell epitope:antibody complex A radio immuno assay that measures the dissociation constant [KD] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|radio immuno assay (RIA)|nM RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex An enzyme-linked immunosorbent assay that measures the dissociation constant [KD] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|ELISA|nM ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex A fluorescence quenching assay that measures the dissociation constant [KD] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|quenching|nM quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A surface plasmon resonance binding assay that measures the association constant [KA] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|surface plasmon resonance (SPR)|1/nM surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|surface plasmon resonance (SPR)|nM surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A fluorescence quenching assay that measures the association constant [KA] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|quenching|1/nM quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex A calorimetric binding assay that measures the association constant [KA] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|calorimetry|1/nM calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex A calorimetric binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|calorimetry|nM calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex An enzyme-linked immunosorbent assay that measures the association constant [KA] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|ELISA|1/nM ELISA measuring the association constant [KA] of a B cell epitope:antibody complex A radio immuno assay that measures the association constant [KA] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|radio immuno assay (RIA)|1/nM RIA measuring the association constant [KA] of a B cell epitope:antibody complex A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) X-ray crystallography [Ã…] obsolete B cell epitope specific X-ray crystallography assay true A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|x-ray crystallography|angstroms X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex A surface plasmon resonance binding assay that measures the off rate [koff] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|surface plasmon resonance (SPR)|1/s surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex A fluorescence quenching assay that measures the off rate [koff] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|quenching|1/s quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex A surface plasmon resonance binding assay that measures the on rate [kon] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB on rate|surface plasmon resonance (SPR)|M^-1s^-1 surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex A fluorescence quenching assay that measures the on rate [kon] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB on rate|quenching|M^-1s^-1 quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1b release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells A flow cytometry assay that detects interleukin-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells An enzyme-linked immunospot assay that detects interleukin-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|ELISPOT ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells A cytometric bead array assay that detects interleukin-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1a release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells An enzyme-linked immunospot assay that detects interferon-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|ELISPOT ELISPOT assay measuring epitope specific interferon-beta production by T cells A flow cytometry assay that detects interferon-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|ICS intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells A flow cytometry assay that detects granulocyte colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB G-CSF release|ICS intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells An enzyme-linked immunosorbent assay that detects interferon-beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNb release|ELISA ELISA measuring epitope specific interferon-beta production by T cells A detection of specific nucleic acid polymers with complementary probes that detects granulocyte colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB G-CSF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells An enzyme-linked immunospot assay that detects granulocyte colony stimulating factor production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB G-CSF release|ELISPOT ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells A cytometric bead array assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL9/MIG release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells rats should be aged between 6 and 8 weeks and weight between 180-250grams A directive information entity which defines and states a principle of standard by which selection process may take place. Person: Philippe Rocca-Serra selection rule OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/ selection criterion An enzyme-linked immunospot assay that detects chemokine (C-X-C motif) ligand 9 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL9/MIG release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 9 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL9/MIG release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 4 production by T cells. IEDB IEDB CCL4/MIP-1b release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 12 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL12/SDF-1 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 13 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL13/BLC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL16 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 21 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL21/SLC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 22 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL22/MDC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells A cytometric bead array assay that detects chemokine (C-C motif) ligand 4 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL4/MIP-1b release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 4 production by T cells. IEDB IEDB CCL4/MIP-1b release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 19 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL19/MIP-3b release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells A flow cytometry assay that detects chemokine (C-C motif) ligand 1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|ICS intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An Investigation agent role borne by a person or organization which is realized in a specimen collection process. Person: Jie Zheng, Chris Stoeckert Penn Group NIAID GSCID-BRC specimen collector role A flow cytometry assay that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|ICS intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells An enzyme-linked immunospot assay that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|ELISPOT ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17F release|biological activity assay measuring epitope specific interleukin-17F production by T cells An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17A release|biological activity assay measuring epitope specific interleukin-17A production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL21/SLC release|biological activity assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL19/MIP-3b release|biological activity assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells. IEDB IEDB CXCL12/SDF-1 release|biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL22/MDC release|biological activity assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL16 release|biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL13/BLC release|biological activity assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells An enzyme-linked immunospot assay that detects macrophage inflammatory protein-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL3/MIP-1a release|ELISPOT ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells A cytometric bead array assay that detects macrophage inflammatory protein-1 gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|cytometric bead array cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells A flow cytometry assay that detects monocyte chemotactic protein-1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|ICS intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells An enzyme-linked immunospot assay that detects monocyte chemotactic protein-1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL2/MCP-1 release|ELISPOT ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells A flow cytometry assay that detects macrophage inflammatory protein-1 gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|ICS intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells An enzyme-linked immunospot assay that detects inflammatory protein-1 gamma production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL9/MIP-1g release|ELISPOT ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells A cytometric bead array assay that detects vascular endothelial growth factor production by T cells. IEDB IEDB VEGF release|cytometric bead array cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor superfamily cytokine production by T cells. IEDB IEDB TNF release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells A flow cytometry assay that detects RANTES production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|ICS intracellular cytokine staining assay measuring epitope specific RANTES production by T cells An enzyme-linked immunospot assay that detects RANTES production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL5/RANTES release|ELISPOT ELISPOT assay measuring epitope specific RANTES production by T cells An enzyme-linked immunospot assay that detects lymphotoxin A production by T cells. IEDB IEDB lymphotoxin A/TNFb release|ELISPOT ELISPOT assay measuring epitope specific lymphotoxin A production by T cells A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL3/MIP-1a release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells A cytometric bead array assay that detects lymphotoxin A production by T cells. IEDB IEDB lymphotoxin A/TNFb release|cytometric bead array cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells A detection of specific nucleic acid polymers with complementary probes that detects lymphotoxin A production by T cells. IEDB IEDB lymphotoxin A/TNFb release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells An enzyme-linked immunospot assay that detects IP-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|ELISPOT ELISPOT assay measuring epitope specific IP-10 production by T cells A flow cytometry assay that detects IP-10 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CXCL10/IP-10 release|ICS intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells An enzyme-linked immunospot assay that detects interleukin-9 production by T cells. IEDB IEDB IL-9 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-9 production by T cells A flow cytometry assay that detects interleukin-9 production by T cells. IEDB IEDB IL-9 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-9 production by T cells. IEDB IEDB IL-9 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells An enzyme-linked immunospot assay that detects interleukin-8 production by T cells. IEDB IEDB IL-8 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-8 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-8 production by T cells. IEDB IEDB IL-8 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells An enzyme-linked immunospot assay that detects interleukin-3 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-3 production by T cells An enzyme-linked immunosorbent assay that detects interleukin-7 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-7 release|ELISA ELISA measuring epitope specific interleukin-7 production by T cells An enzyme-linked immunospot assay that detects interleukin-7 production by T cells. IEDB IEDB IL-7 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-7 production by T cells A flow cytometry assay that detects interleukin-7 production by T cells. IEDB IEDB IL-7 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells A flow cytometry assay that detects interleukin-27 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells A cytometric bead array assay that detects interleukin-3 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-3 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-3 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-3 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells. IEDB IEDB granzyme A release|biological activity assay measuring epitope specific granzyme A release by T cells A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells. IEDB IEDB granulysin release|biological activity assay measuring epitope specific granulysin release by T cells A cytometric bead array assay that detects interleukin-27 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-27 production by T cells A flow cytometry assay that detects interleukin-23 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells An enzyme-linked immunospot assay that detects interleukin-27 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-27 production by T cells An enzyme-linked immunosorbent assay that detects interleukin-27 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-27 release|ELISA ELISA measuring epitope specific interleukin-27 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-18 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-X-C motif) ligand 13 production by T cells An enzyme-linked immunospot assay that detects interleukin-18 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-18 production by T cells A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-X-C motif) ligand 12 production by T cells A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-C motif) ligand 22 production by T cells A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-X-C motif) ligand 16 production by T cells An enzyme-linked immunospot assay that detects interleukin-22 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-22 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-22 production by T cells An enzyme-linked immunospot assay that detects interleukin-23 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-23 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-23 production by T cells A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-C motif) ligand 21 production by T cells A flow cytometry assay that detects interleukin-18 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB (QTT) Date: 2012-11-16; Spreadsheet: All AssayTypes.xls; Worksheet: E specific Template; Mappings: MMExpressionsTcell.txt epitope specific chemokine (C-C motif) ligand 19 production by T cells An enzyme-linked immunospot assay that detects interleukin-21 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-21 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-21 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells A cytometric bead array assay that detects chemokine (C-C motif) ligand 1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 1 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB CCL1/TCA-3 release|ELISPOT ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells An enzyme-linked immunospot assay that detects interleukin-17F production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17F release|ELISPOT ELISPOT assay measuring epitope specific interleukin-17F production by T cells An enzyme-linked immunosorbent assay that detects interleukin-17F production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17F release|ELISA ELISA measuring epitope specific interleukin-17F production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17F production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17F release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells An enzyme-linked immunospot assay that detects interleukin-17A production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17A release|ELISPOT ELISPOT assay measuring epitope specific interleukin-17A production by T cells Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. A planned process in which new information is inferred from existing information. drawing a conclusion A cytometric bead array assay that detects interleukin-18 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-18 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-18 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells An enzyme-linked immunosorbent assay that detects interleukin-16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|ELISA ELISA measuring epitope specific interleukin-16 production by T cells An enzyme-linked immunospot assay that detects interleukin-16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-16 production by T cells A flow cytometry assay that detects interleukin-16 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-16 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17A production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-17A release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells A flow cytometry assay that detects interleukin-1 beta production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-1b release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells An enzyme-linked immunospot assay that detects interleukin-1 beta production by T cells. IEDB IEDB IL-1b release|ELISPOT ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-15 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|RNA/DNA detection detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells An enzyme-linked immunospot assay that detects interleukin-12 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-12 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-12 production by T cells A flow cytometry assay that detects interleukin-15 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells An enzyme-linked immunospot assay that detects interleukin-15 production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IL-15 release|ELISPOT ELISPOT assay measuring epitope specific interleukin-15 production by T cells Zhang, et al. ChIA-PET analysis of transcriptional chromatin interactions. Methods. 2012 Nov;58(3):289-99. [PMID:22926262] An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide. Chris Stoeckert Jie Zheng Venkat Malladi ChIA-PET ChIA-PET assay url:http://en.wikipedia.org/wiki/ChIA-PET chromatin interaction analysis by paired-end tag sequencing assay Yao, et al. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One. 2012;7(9):e46152 [PMID:23029419] An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants. Chris Stoeckert Jie Zheng Venkat Malladi DNA-PET DNA-PET assay PMID:23029419 structural analysis by paired-end tag sequencing assay Ruan, et al. Genome wide full-length transcript analysis using 5' and 3' paired-end-tag next generation sequencing (RNA-PET). Methods Mol Biol. 2012;809:535-62. [PMID:22113299] A transcription profiling by RNA sequencing assay that employs paired-end sequencing of RNA transcripts to determine things such as gene expression, gene structure, and alternative transcript structure. Chris Stoeckert Jie Zheng Michelle Giglio Sebastian Duesing Venkat Malladi RNA-PET RNA-PET assay transcript analysis by paired-end tag sequencing assay A transcription profiling identification objective that aims to characterize the transcription start sites of genes. Person: Chris Stoeckert, Jie Zheng Penn Group transcription start site identification objective A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process. Person: Venkat Malladi, Jie Zheng Venkat Malladi, Jie Zheng ENCODE project paired-end library preparation Sabo, et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16837-42. [PMID:15550541] An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I. Chris Stoeckert Jie Zheng Venkat Malladi url:http://en.wikipedia.org/wiki/DNase-Seq DNase I hypersensitive sites sequencing assay A sequence feature identification objective that aims to characterize the interactions between protein and RNA. JZ: Term added for ENCODE project requested assays. Definition adapted from 'protein and DNA interaction identification objective'. Person: Jie Zheng Jie Zheng protein and RNA interaction identification objective Zhao et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell (2010) vol. 40 (6) pp. 939-53 [PMID:21172659] An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs). Chris Stoeckert Jie Zheng Venkat Malladi RIP-seq RIP-seq assay PMID:21172659 RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay Heulga et al. Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep. 2012 Feb 23;1(2):167-78. [PMID:22574288] An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein. Chris Stoeckert Jie Zheng Venkat Malladi CLIP-seq CLIP-seq assay HITS-CLIP PMID:18978773 cross-linking immunoprecipitation high-throughput sequencing assay Giresi, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17 (6): 877_�_85. [PMID:17179217] An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity. Chris Stoeckert Jie Zheng Venkat Malladi FAIRE-seq FAIRE-seq assay url:http://en.wikipedia.org/wiki/FAIRE-Seq formaldehyde-assisted isolation of regulatory elements assay Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842] An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA. Chris Stoeckert Jie Zheng Venkat Malladi MRE-seq MRE-seq assay PMID:20613842 methylation-sensitive restriction enzyme sequencing assay Meissner et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18): 5868_�_5877. [PMCID: PMC1258174] A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome. Chris Stoeckert Jie Zheng Venkat Malladi RRBS RRBS assay reduced representation bisulfite-seq PMC:1258174 reduced representation bisulfite sequencing assay Cokus et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13;452(7184):215-9. [PMID:18278030]. A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing. Chris Stoeckert Jie Zheng Venkat Malladi Shotgun bisulfite sequencing WGBS WGSBS whole genome bisulfite sequencing whole-genome shotgun bisulfite sequencing PMID:18278030 shotgun bisulfite-seq assay Batut et al. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Research. 2013 Jan;23(1):169-80. [PMID:22936248] A transcription profiling by RNA sequencing assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing. Chris Stoeckert Jie Zheng Michelle Giglio Sebastian Duesing Venkat Malladi RAMPAGE PMID:22936248 RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Penn Group assay array secondary cultured cell A cultured cell that has been passaged or derives from a cell that has been passaged in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. Person: Matthew Brush PERSON: Matthew Brush A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. secondary cultured cell establishing cell line a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset). 2013-4-20 MHB: For cases of initial establilshment of a line from a primary culture, successive passaging and/or selection processes can confer increasing degrees of genetic stability and compositional homogeneity as compared to the input primary culture. Historically, many texts consider the first passage as the clearest point to define the beginning of a line. However, in practice it is more often that case that more than one passage, and possibly additional selective techniques, may be required before a culture is deemed to have sufficient stability and homogeneity to be considered cell line. This is the view taken in OBI. Regardless, what is important is that some intentional, experimental step has been taken to establish a more homogenous and stable culture that can be characterized and progatated over time. Person: Matthew Brush PERSON:Matthew Brush establishing cell line A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants. MHB 3-22-13: Discussions are ongoing about the label of this class, given consideration of a second class that covers nucleic acid parts of cells or virions that participate in gene expression processes as a template for expression or a direct effector of expression of some other genetic element (e.g. an siRNA), but are not necessarily heritable by progeny or inherited from ancestors. So things like transiently transfected plasmids and siRNAs would qualify as instances of this second class, but not of 'genetic material' as defined here. Also, OBI needs to import a class representing virions for an axiom on genetic material (part_of some (cell or virion). genomic material hereditary genetic material OBI developer calls, March 4 2013 and March 11 2013 Naturally occurring or experimentally incorporated nucleic acids that meet these criteria can qualify as genetic/genomic material. Qualifying examples include: (1) inherited chromosomal DNA in germ cells, stem cells, fully differentiated cells, or cell line cells, or the DNA/RNA content of a virion; (2) natural replicons exchanged through horizontal gene transfer mechanisms such as bacterial conjugation, which are capable of replication and inheritance by progeny; (3) a chromosomally integrated gene targeting DNA construct transfected into a cell; or (4) a stable extra-chromosomal replicon delivered into cells, such as a plasmid in bacterial host with ori allowing indefinite propagation. Non-qualifying examples include a transiently transfected plasmid or siRNA oligo (as these are not able to be replicated and inherited by progeny cells). genetic material An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi http://www.illumina.com/technology/beadarray_technology.ilmn Illumina BeadChip A BeadChip made for an analyte assay that generates information about DNA methylation. PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Penn Group Illumina methylation BeadChip A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. Anna Maria Masci http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg LSRFortessa X-20 A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs). PRS/AGB: changed to restrictions by adding 2 possible specified outputs (N50 and genome coverage) for sequence assembly. Alejandra Gonzalez-Beltran PERSON: Jie Zheng, Chris Stoeckert Philippe Rocca-Serra NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence assembly process Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. see table2 a data item that is the number of times that a given process failed, as an integer Alejandra Gonzalez-Beltran Philippe Rocca-Serra PRS, AGB number of errors Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "However, the error correction module in SOAPdenovo was designed for short Illumina reads (35-50 bp), which consumes an excessive amount of computational time and memory on longer reads, for example, over 150 GB memory running for two days using 40-fold 100 bp paired-end Illumina HiSeq 2000 reads" random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation Alejandra Gonzalez-Beltran Philippe Rocca-Serra PRS, AGB random access memory size cultured immune cell population a cultured cell population comprised of a single type of immune system cell MHB 3-5-13: created as a (temporary) organizational class to organize IEDB immune cultured cell population types. These were all previously labled as 'cell cultures' - and relabeld here as 'cultured cell populations' since a CLO alignment outcome was to use the term 'cell culture' to refer to cultured cells + media. Consult with BP as to whether this organizational class is useful and if so, how to define it. Also check whether the intent was to represent cell populations rather than cell cultures. PERSON:Matthew Brush immune cell culture sample PERSON:Matthew Brush cultured immune cell population cell culture A material entity comprised of cultured cells and the media in which they are being propagated or stored. PERSON:Matthew Brush OBI-CLO Alignment Working Group (Spring 2013) A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored. cell culture Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location Alejandra Gonzalez-Beltran Philippe Rocca-Serra RAM http://en.wikipedia.org/wiki/RAM last accessed: 2013-12-02 random access memory establishing primary cell culture 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. an establishing cell culture process whereby cells explanted directly from an organismal source or specimen, and placed in culture for maintenance or propagation as a primary cell culture PERSON: Matthew Brush Cells are originally plated at a certain concentration referred to as seeding density. Upon a first passage this primary culture becomes a secondary cell culture that can be propagated to become a stable and homogneous cell line. This class covers establishment of primary cultures from any native cell - 'in vivo' cells isolated from some multicellular organism, or 'in environment' unicellular organisms isolated from some natural environment. establishing primary cell culture A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output. 2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device. PERSON:Matthew Brush PERSON:Matthew Brush (copied from ReO) Reagents are distinguished from devices/instruments that also serve as facilitators in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, devices do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance can only realize one of these roles in the execution of a given assay. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique: note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is that of some modified cell specimen which shares identity with the input unmodified cell specimen, and not with the biotin label. Thus, we see that an important criteria of 'reagent-ness' is that it is a facilitator, and not the primary focus of an investigation or material processing technique (ie not the specified subject/evaluant about which knowledge is sought, or the specified output material of the technique). reagent An organization that is the affiliation of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's Institution NIAID GSCID-BRC organization of specimen provider principal investigator An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's Institution NIAID GSCID-BRC organization of Bioinformatics Resource Center contact person Some examples of target material are Genome, Purified chromosome, Transcriptome, Phenotype, Proteome. A plan specification which specifies the type of material that will be assayed in an investigation. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Material NIAID GSCID-BRC target material in specimen specification A person who is the contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact Name NIAID GSCID-BRC Bioinformatics Resource Center contact person Some examples of specimen scope are Monoisolate, Multiisolate, Multi-species, Environment, or Synthetic. A plan specification which specifies the scope of an investigation based on the heterogeneity of organisms or type of material that are the specified input of specimen collection. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Scope NIAID GSCID-BRC specimen-based scope of investigation specification An organization that provides a service to store and distribute specimens PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository NIAID GSCID-BRC specimen repository organization An email address of the person who is contact representative of a Bioinformatics Resource Center PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Bioinformatics Resource Center Contact's email NIAID GSCID-BRC email address of Bioinformatics Resource Center contact person A person who is the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact Name NIAID GSCID-BRC sequencing facility contact person A person who is a principal investigator and provides the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider Principal Investigator (PI) Name NIAID GSCID-BRC specimen provider principal investigator An email address of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's email NIAID GSCID-BRC email address of specimen collector An organization that provides sequence determination service PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility NIAID GSCID-BRC sequencing facility organization Some examples of Project Objectives are Raw sequence reads, Sequence, Analysis, Assembly, Annotation, Variation, Epigenetic markers, expression, maps, phenotype An objective specification which indicates the type of data that will be generated and submitted to a database. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Objectives NIAID GSCID-BRC specification of data to be generated in an investigation An organization that is the affiliation of the person collecting the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector's Institution NIAID GSCID-BRC organization of specimen collector An email address of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's email NIAID GSCID-BRC email address of sequencing facility contact person A person who collects the specimen PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Collector Name NIAID GSCID-BRC specimen collector Some examples of Project Method are Sequence, Array, Mass Spectrometry A plan specification which indicates the assay type used to obtain data. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Project Method NIAID GSCID-BRC investigation assay specification An organization that is the affiliation of the contact representative at the sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sequencing Facility Contact's Institution NIAID GSCID-BRC organization of sequencing facility contact person A textual entity that is about any of the aspects of an investigation worth noting PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Comments NIAID GSCID-BRC comment on investigation Some examples of target capture are Whole, CloneEnds, Exome, TargetedLocusLoci, RandomSurvey A plan specification which specifies how the material enrichment procedure will influence the scale, or type of material that will be assayed in the specimen. PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Target Capture NIAID GSCID-BRC target capture specification A specimen identifier which is assigned by a specimen repository PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Specimen Repository Sample ID NIAID GSCID-BRC specimen identifier assigned by specimen repository A specimen identifier which is assigned by a sequencing facility PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample ID - Sequencing Facility NIAID GSCID-BRC specimen identifier assigned by sequencing facility A sample preparation for assay that preparation of nucleic acids for a sequencing assay PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Nucleic Acid Preparation Method NIAID GSCID-BRC sample preparation for sequencing assay An email address of the principal investigator providing the specimens for the investigation PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group Sample Provider PI's email NIAID GSCID-BRC email address of specimen provider principal investigator A service provides sequencing service which is the realization of some sequencing such as RNA and DNA sequencing in which the service provider role is realized. Person: Jie Zheng Adpated from 'DNA sequencing service' NIAID GSCID-BRC sequencing service secondary cultured cell population A cultured cell population that is derived through one or more passages in culture. The term 'secondary cell culture' is generally used in biological texts/protocols to refer to any culture of cells following an initial passage. We include it here because there are often a number of passages between a primary culture and the establishment of a stable, homogenous cell line. Such cultures are considered to be 'secondary cultures' but not 'cell lines' during this intermediate passaging/selection period between their derivation from a 'primary cell culture' and derivation into a 'cell line', which is a more specific type of secondary culture. PERSON:Matthew Brush secondary cell culture sample PERSON:Matthew Brush The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. secondary cultured cell population cancer cell line An immortal cell line derived from a transformed cell that was part of a malignant tumor. cancer cell line immortalizing cell line transformation a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture immortalizing cell line transformation that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 An information content entity that expresses an assertion that is intended to be tested. In the Philly 2013 workshop, we recognized the limitations of "hypothesis textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group hypothesis Group:2013 Philly Workshop group testable hypothesis The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on data primary cell culture A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored. PERSON:Matthew Brush OBI-CLO Alignment Working Group (Spring 2013) primary cell culture cell line culture A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently stored. PERSON:Matthew Brush OBI-CLO Alignment Working Group (Spring 2013) A cell line culture includes the cells in culture, as well as the media and all additives/reagents in which the cells are being grown or in which they are stored. cell line culture cell freezing medium A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles. PERSON: Matthew Brush cell freezing medium Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. See Table 4 computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency. Alejandra Gonzalez-Beltran Philippe Rocca-Serra computation run time datum PRS,AGB computation run time A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation. Chris Stoeckert, Jie Zheng LMA MLPA Multiplex ligation-dependent probe amplification web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification Pubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/ multiplex ligation-mediated amplification Hiranti et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 2008 October 7;6(10):e245 [PMID:18842067] An assay which quantifies the timing of DNA replication as a function of genome position using array technology. Chris Stoeckert Jie Zheng Venkat Malladi Repli-chip Repli-chip assay PMID:18842067 DNA replication timing by array assay A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time. Chris Stoeckert, Jie Zheng Group: Penn Group DNA replication identification objective A molecular feature identification objective that aims to determine spatial organization of chromatin. Chris Stoeckert, Jie Zheng Group: Penn Group chromosome conformation identification objective Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs). Chris Stoeckert Jie Zheng Venkat Malladi RIP-chip RIP-chip assay PMID:21125495 RNA-binding protein immunoprecipitation array profiling assay van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094] An assay that measures the organization of chromosomes at the genome-wide scale. Chris Stoeckert Jie Zheng Venkat Malladi 5C 5C assay PMID:16954542 Carbon-copy chromosome conformation capture assay Hansen et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 January 5; 107(1): 139_�_144. [PMID:19966280] An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing. Chris Stoeckert Jie Zheng Venkat Malladi Repli-seq Repli-seq assay PMID:19966280 DNA replication timing by sequencing assay Jain et al. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. [PMID:21125495] An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs). Chris Stoeckert Jie Zheng Venkat Malladi PMID:21125495 RNA-binding protein immunoprecipitation tiling array profiling assay Juhlia et al. MicroRNA expression profiling reveals miRNA families regulating_specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011;6(6). PMID: 21731767 A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology. Chris Stoeckert Jie Zheng Venkat Malladi miRNA-HTS miRNA-seq microRNA-seq microRNA-seq assay url:http://www.ebi.ac.uk/efo/EFO_0002896 microRNA profiling by high throughput sequencing assay Taylor et al.Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem. 2001 Jun;73(11):2594-604. [PMID:11403305] A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation. Chris Stoeckert Jie Zheng Venkat Malladi PMID:3462691 protein sequencing by tandem mass spectrometry assay Cui et al.Genome-wide approaches to determining nucleosome occupancy in metazoans using MNase-Seq. Methods Mol Biol. 2012;833:413-9. [PMID:22183607] An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease Chris Stoeckert Jie Zheng Venkat Malladi MNase-seq MNase-seq assay PMID:17038564 micrococcal nuclease digestion followed by high throughput sequencing assay Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082] A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site Bjoern Peters Chris Stoeckert Jie Zheng Venkat Malladi ChIP-exo assay PMID:22153082 chromatin immunoprecipitation with exonuclease sequencing assay A transcription profiling assay that quantifies the microRNA species within a biological sample. Chris Stoeckert Jie Zheng Venkat Malladi miRNA expression assay microRNA expression assay PMID: 23382819 microRNA profiling assay PMID: 24023800. In this study, a set of eleven genes (VATP16, 60 S, UQCC, SMD3, EF1α, UBQ, SAND, GAPDH, ACT, PsaB, PTB2) was evaluated to identify reference genes during the first hours of interaction (6, 12, 18 and 24 hpi) between two V. vinifera genotypes and P. viticola. Two analyses were used for the selection of reference genes: direct comparison of susceptible, Trincadeira, and resistant, Regent, V. vinifera cultivars at 0 h, 6, 12, 18 and 24 hours post inoculation with P. viticola (genotype effect); and comparison of each genotype with mock inoculated samples during inoculation time-course (biotic stress effect). Three statistical methods were used, GeNorm, NormFinder, and BestKeeper, allowing to identify UBQ, EF1α and GAPDH as the most stable genes for the genotype effect. A planned process with the objective to create a group of entities by applying a predefined criteria to a larger group of entities. this term refers to a planned process and therefore is distinct from the notion of 'natural selection', a process covering the operation of natural causes by which those individuals of a species that are best adapted to the environment tend to be preserved and to transmit their characters, while those less adapted die out, so that in the course of generations the degree of adaptation to the environment tends progressively to increase. (as defined by Oxford English Dictionary) Person: Philippe Rocca-Serra selection process OBI selection A value specification that specifies the mass of some thing. PERSON:Bjoern Peters mass value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification 1 1 A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification A planned process in which predicted values for some thing are compared to measured values for that thing. comparing prediction to measurement The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error. PERSON:Bjoern Peters predicted value A predicted value where the prediction specifies the mass of some thing. PERSON:Bjoern Peters predicted mass value molecular-labeled material a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay PERSON:Matthew Brush OBI developer call, 3-12-12 molecular-labeled material Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "The genome coverage increased from 81.16% to 93.91%" A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%. Alejandra Gonzalez-Beltran Philippe Rocca-Serra A beginner's guide to eukaryotic genome annotation. Yandell M, Ence D. Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174. PMID: 22510764 genome coverage Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" the weighted median item size or N50 is a weighted median of the lengths of items, equal to the length of the longest item i such that the sum of the lengths of items greater than or equal in length to i is greater than or equal to half the length of all of the items. With regard to assemblies the items are typically contigs or scaffolds. It therefore denotes the ability of the software to create contigs and provides information about the resulting sequence assembly Alejandra Gonzalez-Beltran Philippe Rocca-Serra weighted median item size adapted from: "http://genome.cshlp.org/content/21/12/2224.full?sid=74019122-f944-4ccc-bffe-d16fdd0e7d6c" (from table 7) and from "http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html" N50 Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" N50 statistic computed for the contigs produced by the assembly process. A contig N50 is calculated by first ordering every contig by length from longest to shortest. Next, starting from the longest contig, the lengths of each contig are summed, until this running sum equals one-half of the total length of all contigs in the assembly. The contig N50 of the assembly is the length of the shortest contig in this list. Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html contig N50 An organization that provides funding support for projects such as investigations. PERSON: Jie Zheng, Chris Stoeckert funding organization NIAID GSCID-BRC metadata working group NIAID GSCID-BRC grant agency 'funding organization' http://vivoweb.org/ontology/core#FundingOrganization A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements. PERSON: Jie Zheng, Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Pipeline_%28software%29 NIAID GSCID-BRC software pipeline A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence annotation Gigascience. 2012 Dec 27;1(1):18. doi: 10.1186/2047-217X-1-18. PMID: 23587118. "Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp" N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: nature:http://www.nature.com/nrg/journal/v13/n5/box/nrg3174_BX1.html scaffold N50 SP6 promoter, forward primer (SP6 TTTAGGTGACACTATAG) A short oligonucleotide complementary to target DNA (5'->3' on plus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm. Philippe Rocca-Serra 5' primer forward primer sense primer adapted from http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p forward PCR primer A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group annotation provider NIAID GSCID-BRC sequence annotation provider A textual entity that is used to denote a sequence assembly. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group assembly name NIAID GSCID-BRC sequence assembly name A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence. PERSON: Jie Zheng, Chris Stoeckert NIAID GSCID-BRC metadata working group NIAID GSCID-BRC sequence annotation reporting role 5' end of luciferase, reverse primer (LucNrev CCTTATGCAGTTGCTCTCC) A short oligonucleotide complementary to target DNA (5'->3' on minus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm. Philippe Rocca-Serra 3' primer antisense primer reverse primer adapted from "http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/Glossary.shtml#p" reverse PCR primer A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C. Person: Mathias Brochhausen, Jie Zheng WEB: http://en.wikipedia.org/wiki/Flash_freezing flash freezing A planned process with the objective to bring some material entity to a temperature below its freezing point. Person: Mathias Brochhausen, Jie Zheng Mathias Brochhausen freezing PMID: 6379641 An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed Bjoern Peters Philippe Rocca-Serra chromatin immunoprecipitation assay url:https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation ChIP assay competitive binding reference ligand role The role of a radiolabeled peptide that is known to bind to the MHC molecule HLA-A*02:01 with high affinity when it is used in a competitive binding assay in which another peptide of interest is tested for its ability to outcompete binding of the labeled peptide in a dose dependent fashion. A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target. Bjoern Peters, Randi Vita, James A. Overton Bjoern Peters competitive binding reference ligand role http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation Philippe Rocca-Serra http://sourceforge.net/p/obi/obi-terms/707/ assay using chromatin immunoprecipitation A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision. Person: Jie Zheng MO_734 hardware_variation_design hardware testing design systematic review study design Red blood cell transfusion in patients with traumatic brain injury: a systematic review protocol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4090399/ The effect of moderate gestational alcohol consumption during pregnancy on speech and language outcomes in children: a systematic review. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3892059/ A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed. PERSON: Bill Hogan systematic review study design http://www.illumina.com/technology/multiplexing_sequencing_assay.ilmn A planned process which consists in running a set of samples as a pool on a sequencing instrument, while retaining the ability to associate individual results to each of the individual input samples through the use of a ligated oligonucleotide (the "multiplex identifier sequence"). This oligonucleotide is introduced during the sequence library preparation, and is unique to and specific for all library fragments derived from each sample in a sample pool. Dan Berrios PERSON:Philippe Rocca-Serra OBI multiplexed nucleotide library sequencing PMID:20679230 PMID:25367129 An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity. Philippe Rocca-Serra environmental gene survey targeted gene survey targeted gene survey DNA barcoding OBI taxonomic diversity assessment by targeted gene survey https://www.neb.com/protocols/1/01/01/taq-dna-polymerase-with-standard-taq-buffer-m0273 a PCR program is a plan specification which is executed during a polymerase chain reaction (PCR) by a thermocycler instrument that will iterate through the changes in temperature and duration of each of the annealing, denaturation, elongation steps for as many times as specified by the program. PERSON:Philippe Rocca-Serra OBI PCR program http://www.ncbi.nlm.nih.gov/pubmed/25367129 "performing a profiling of microbial phylogenetic composition using sequencing of 16S rRNA gene (used as target gene) is a directive information specifying a coding genomic region which is the focus of a planned process such as an assay, for instance in a environmental gene survey PERSON:Philippe Rocca-Serra PRS for OBI target gene target gene specification http://www.ncbi.nlm.nih.gov/pubmed/23335919 "performing a profiling of microbial phylogenetic composition using massively-parallel pyrotag sequencing targeting the V9 hypervariable region (used as target subfragment) of the 18S ribosomal RNA (rRNA) gene (used as target gene) is a directive information specifying a genomic region, possibly located in a coding genomic region, which is the focus of a planned process such as an assay, for instance in a environmental gene survey PERSON:Philippe Rocca-Serra PRS for OBI target subfragment target subfragment specification decision-theoretic analysis objective An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric. The best action to take is typically defined as the one that maximizes expected utility. PERSON: Bill Hogan decision analysis objective PERSON: Bill Hogan decision-theoretic analysis objective decision analysis study design a study design that has a decision analysis objective specification as part PERSON: Bill Hogan PERSON: Bill Hogan decision analysis study design is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to separate all reads belonging to a given single sample following the sequencing of a multiplexed library PERSON: Philippe Rocca-Serra PRS for OBI sequence library data demultiplexing We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. in http://www.ncbi.nlm.nih.gov/pubmed/22574170 A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library PERSON:Philippe Rocca-Serra OBI multiplexing sequence identifier http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1610290/ Operational Taxonomic Unit matrix is a data item, organized as a table, where organismal taxonomic units, computed by sequence analysis and genetic distance calculation, are counted in a set of biological or environmental samples. The table is used to appraise biodiversity of a population or community of living organism. PERSON:Philippe Rocca-Serra PRS for OBI operational taxonomic unit matrix biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level PERSON:Philippe Rocca-Serra PRS for OBI biodiversity assessment objective http://www.ncbi.nlm.nih.gov/pubmed/24997861 Nat Methods. 2014 Aug;11(8):834-40. doi: 10.1038/nmeth.3022. Epub 2014 Jul 6. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. a multiplexed library is a material entity which is the output of a library preparation process that uses a ligation step to attach a unique multiplexing sequence identifier to a specific sample, then mixes several such tagged samples prior to the library amplification process proper. A multiplexed library allows the sequencing of several samples in one sequencing run. PERSON:Philippe Rocca-Serra DNA-barcoded sequencing library PRS for OBI multiplexed sequencing library Ion 316 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ PERSON: Sagar Jain Ion 316 Chip Ion PGM 316 Chip Ion PGM 316 Chip v2 http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html Ion 316 Chip v2 Ion 318 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ PERSON: Sagar Jain Ion 318 Chip Ion PGM 318 Chip Ion PGM 318 Chip v2 http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html Ion 318 Chip v2 ion semiconductor chip An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface. Issue Tracker: #776 https://sourceforge.net/p/obi/obi-terms/776/ PERSON: Sagar Jain ion chip ion integrated circuit ion semiconductor http://www.thefreedictionary.com/Semiconductor+chip ion semiconductor chip Ion 314 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb. Issue Tracker #766 https://sourceforge.net/p/obi/obi-terms/766/ PERSON: Sagar Jain Ion 314 Chip Ion PGM 314 Chip Ion PGM 314 Chip v2 http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html Ion 314 Chip v2 Performing deuterium exchange on a protein by itself and in the presence of a binding partner, degrading the protein into peptide segments and identifying where deuterium exchange occurred by detecting the peptides in Mass Spectrometry. Peptides that have a modified deuteration pattern when the protein was bound to a partner are expected to be part of the binding interface. A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure. IEDB IEDB hydrogen/deuterium exchange footprinting assay An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells. An assay that counts and/or measures characteristics of cells. IEDB IEDB cytometry assay An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules. IEDB IEDB immunoblot assay A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other. IEDB IEDB fluorescence quenching binding assay Comparing the level of allergy symptoms in humans before and post allergy immunotherapy. Testing if injection of a chemical compound into mice will lead to decreased survival. An assay in which the effect of a targeted process (the intervention) on an organism is tested. The intervention in an experiment should be modeled accordingly to the intevention carried out in a human cllinical trial, which is currently modeled as 'study intervention'. This touches the boundaries of study vs. assay. IEDB IEDB in vivo intervention experiment Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was more severe than the disease course of a set of mice that were not injected with the same peptide. An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host. Should have data about disease severity as readout; could just use disease for now IEDB IEDB disease exacerbation in vivo intervention experiment Injecting a set of mice with a peptide and measuring symtoms to determine if their disease course was less severe than the disease course of a set of mice that were not injected with the same peptide. An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host. should have challenge as intervention IEDB IEDB protection from challenge in vivo intervention experiment Injecting a set of mice with a Der p 2 peptide and measuring the IL-2 response of T cells from those mice when exposed to the Der p 2 protein in vitro to determine if those T cells made less IL-2 than cells taken from mice which were not injected with the same Der p 2 peptide. An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response. should have tolerance induction as intervention IEDB IEDB tolerance induction intervention experiment Testing if administering oral histamine-blockers will reduce the number of emergency room visits in severely asthmatic individuals. An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested. should have treatment as intervention IEDB IEDB treatment intervention experiment Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray. An analyte assay where binding of the analyte to immobilized matrix is measured. IEDB IEDB microarray assay Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques. An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section. IEDB IEDB immunohistochemistry A MHC binding constant determination assay measuring equilibrium association constant (KA). IEDB IEDB association constant KA|binding assay|1/M assay measuring the association constant [KA] of a MHC:ligand complex A MHC binding constant determination assay measuring equilibrium dissociation constant (KD). IEDB IEDB dissociation constant KD|binding assay|nM assay measuring the dissociation constant [KD] of a MHC:ligand complex A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation. IEDB IEDB dissociation constant KD|purified MHC/direct/radioactivity|nM radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex A MHC binding constant determination assay measuring half life of binding. IEDB IEDB half life|binding assay|min assay measuring the half life of a MHC:ligand complex A MHC binding constant determination assay measuring half maximal effective concentration (EC50). IEDB IEDB half maximal effective concentration (EC50)|binding assay|nM assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50). IEDB IEDB half maximal inhibitory concentration (IC50)|binding assay|nM assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex A MHC binding constant determination assay measuring binding off rate measurement data item (koff). IEDB IEDB off rate|binding assay|1/s assay measuring the off rate measurement [koff] of a MHC:ligand complex A MHC binding constant determination assay measuring binding on rate (kon). IEDB IEDB on rate|binding assay|nM^-1s^-1 assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex An analytical chromatography assay that measures the association constant [KA] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|chromatography|1/nM chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex An analytical chromatography assay that measures the dissociation constant [KD] of an antigen binding with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|chromatography|nM chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A hydrogen/deuterium exchange footprinting assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, James Overton, Bjoern Peters IEDB qualitative binding|hydrogen/deuterium exchange footprinting assay hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex A immunohistochemistry assay that detects the binding of an antigen with an antibody. IEDB IEDB qualitative binding|immunohistochemistry immunohistochemistry assay measuring binding of a B cell epitope:antibody complex A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a T cell epitope:MHC:TCR complex. IEDB IEDB 3D structure|any method 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. "Lane-by-lane sequencing using Illumina's Genome Analyzer II." BioTechniques 54.5 (2013): 265-269. PMID: 23662897 An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Genome Analyzer IIx Illumina GA IIx ENCODE group Illumina Genome Analyzer IIx Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013 May;3:1843. PMID:23673380 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng HiSeq 2000 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Illumina HiSeq 2000 Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg HiSeq 2500 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf Illumina HiSeq 2500 Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, Yoon IK, Klungthong C, Fernandez S. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform. J Virol Methods. 2013 Nov;193(2):394-404. [PMID:23856301] A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng MiSeq http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf Illumina MiSeq Naumov, Vladimir A., et al. "Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips." Epigenetics 8.9 (2013): 0-1. PMID: 23867710 A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Infinium Human Methylation 450K BeadChip http://www.illumina.com/products/methylation_450_beadchip_kits.ilmn Methylation 450K BeadChip Polidoro, Silvia, et al. "Effects of bisphosphonate treatment on DNA methylation in osteonecrosis of the jaw." Mutation Research/Genetic Toxicology and Environmental Mutagenesis 757.2 (2013): 104-113. PMID: 23892139 A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Infinium Human Methylation 27K BeadChip http://res.illumina.com/documents/products/datasheets/datasheet_dna_methylation_analysis.pdf Methylation 27K BeadChip Edwards, Todd L., et al. "Genome-Wide Association Study Confirms SNPs in SNCA and the MAPT Region as Common Risk Factors for Parkinson Disease." Annals of human genetics 74.2 (2010): 97-109. PMID: 20070850 A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina Human 1M-Duo Infinium HD BeadChip http://www.illumina.com/technology/infinium_hd_assay.ilmn 1M-Duo Infinium HD BeadChip Vissers, Lisenka ELM, et al. "A de novo paradigm for mental retardation." Nature genetics 42.12 (2010): 1109-1112. PMID:21076407 A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Applied Biosystems SOLiD 3 Plus System http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_072050.pdf SOLiD 3 Plus System Miller, Becky Akiko. Detection and biological assessment of genome structural variation in Plasmodium falciparum. Diss. University of Notre Dame, 2012. http://etd.nd.edu/ETD-db/theses/available/etd-04182012-114744/ A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Mouse 385K Whole Genome CGH Tiling Array http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Mouse 385K Whole Genome CGH Tiling Array Wartman, Lukas D., et al. "Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression." The Journal of clinical investigation 121.4 (2011): 1445. PMID:21436584 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Mouse 3x720K Whole Genome CGH Tiling Array Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism PMID:21091464 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Human 3x720K Whole Genome CGH Tiling Array http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Human 3x720K Whole Genome CGH Tiling Array Filges, Isabel, et al. "Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome." Journal of medical genetics 48.2 (2011): 117-122. PMID:21037274 A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0 http://www.nimblegen.com/downloads/support/05434483001_NG_CGHLOH_UGuide_v9p1.pdf Human 2.1M Whole-Genome CGH Tiling Array v2.0 Spaethling, Jennifer M., and James H. Eberwine. "Single-cell transcriptomics for drug target discovery." Current opinion in pharmacology (2013). pmid:23725882 A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg Pacific Biosciences RS II http://www.pacificbiosciences.com/products/ PacBio RS II Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 A human array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller removed "V2" per https://github.com/obi-ontology/obi/issues/831 on 20180511. https://www.nanostring.com/products/mirna-assays/mirna-panels nCounter Human miRNA Expression array An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies. Chris Stoeckert Jie Zheng DNA methylation ChIP-chip Penn group DNA methylation profiling by ChIP-chip assay A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS). Chris Stoeckert Jie Zheng expression MPSS url:http://en.wikipedia.org/wiki/Massively_parallel_signature_sequencing transcription profiling by MPSS assay An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques. Chris Stoeckert Jie Zheng histone modification ChIP-chip Penn group histone modification identification by ChIP-chip assay An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques. Chris Stoeckert Jie Zheng histone modification ChIP-Seq Penn group histone modification identification by ChIP-Seq assay A transcription factor binding site assay that utilizes ChIP-chip technology. Chris Stoeckert Jie Zheng TF Binding ChIP-chip Penn group transcription factor binding site identification by ChIP-chip assay A transcription factor binding site assay that utilizes ChIP-seq technology. Chris Stoeckert Jie Zheng TF Binding ChIP-Seq Penn group transcription factor binding site identification by ChIP-Seq assay An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation. Chris Stoeckert Jie Zheng Penn group epigenetic modification assay A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng NextSeq 500 http://systems.illumina.com/systems/nextseq-sequencer.html Illumina NextSeq 500 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng HiSeq 1000 http://res.illumina.com/documents/products/datasheets/datasheet_hiseq_systems.pdf Illumina HiSeq 1000 A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix HT Human Genome U133 Plus 2 Array Plate Set HG-U133 Plus 2 HG-U133 Plus 2 array http://www.affymetrix.com/estore/esearch/search.jsp?pd=131455&N=4294967292 Human Genome U133 Plus 2.0 tiling array An AB SOLid System which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Applied Biosystems SOLiD 4 System SOLiD 4 http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing/next-generation-systems/solid-4-system.html?CID=FL-091411_solid4 SOLiD 4 System A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix Human Exon 1.0 St Array Human Exon 1.0 Human Exon 1.0 ST Array http://www.affymetrix.com/catalog/131453/AFFY/Human+Gene+ST+Arrays#1_1 Human Exon 1.0 ST tilling array A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Affymetrix HT Human Genome U133 Array Plate Set HG-U133 HG-U133 array http://www.affymetrix.com/estore/esearch/search.jsp?pd=131441&N=4294967292 Human Genome U133 tiling array An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories. Person: Venkat Malladi, Chris Stoeckert, Jie Zheng Genome Analyzer IIe Illumina GA IIe http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf Illumina Genome Analyzer IIe A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library. Related tracker:https://sourceforge.net/p/obi/obi-terms/720/ Person:Chris Stoeckert PMID:15905473 SAGE ditag library preparation PMID:15905473 A transcription profiling by RNA sequencing assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule that is then sequenced. Chris Stoeckert Janos Demeter Jie Zheng Michelle Giglio Sebastian Duesing SAGE PMID:7570003 https://sourceforge.net/p/obi/obi-terms/720/ serial analysis of gene expression assay PMID:19521816 A genotyping by array assay that uses tiling array technology. Chris Stoeckert Janos Demeter Jie Zheng DNA sequence variation detection by tiling array PMID:19521816 https://sourceforge.net/p/obi/obi-terms/720/ genotyping by tiling array assay PMID:20080586 A genotyping by array assay that uses SNP array technology. Chris Stoeckert Janos Demeter Jie Zheng DNA sequence variation detection by snp array PMID:20393561 https://sourceforge.net/p/obi/obi-terms/720/ genotyping by SNP array assay pmid:20811459 A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes Chris Stoeckert Janos Demeter PARS PMID:20811459 https://sourceforge.net/p/obi/obi-terms/725/ parallel analysis of RNA structure assay pmid:23580730 A translation profiling assay that combines transcript leader sequencing with polysome fractionation. TATL-seq works by applying TL-seq across fractions of a polysome gradient, generating TL-specific translational measurements to identify how different transcript leader sequences effect translation. Chris Stoeckert Janos Demeter TATL-seq PMID:23580730 http://hdl.handle.net/1721.1/83763 https://sourceforge.net/p/obi/obi-terms/725/ translation-associated transcript leader sequencing assay pmid:23580730 A transcription profiling by RNA sequencing assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. Chris Stoeckert Janos Demeter Michelle Giglio Sebastian Duesing TL-seq PMID:23580730 https://sourceforge.net/p/obi/obi-terms/725/ transcript leader sequencing assay A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein. Chris Stoeckert Janos Demeter PMF protein fingerprinting ERO:0001668 url:http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting https://sourceforge.net/p/obi/obi-terms/725/ peptide mass fingerprinting assay pmid:23580730 An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray. Chris Stoeckert Janos Demeter OBI:0000870 https://sourceforge.net/p/obi/obi-terms/725/ array based nucleic acid structure mapping assay pmid:17873876 An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays Chris Stoeckert Janos Demeter https://sourceforge.net/p/obi/obi-terms/725/ micrococcal nuclease digestion followed by tiling array assay Aspden et al., (August 2014). "Extensive translation of small open reading frames revealed by poly-ribo-seq." eLIFE 2014;3:e03528 A translation profiling assay that sequences only mRNA protected by the ribosome during translation and thus provides information on which transcipts are undergoing active translation. Chris Stoeckert Jie Zheng Michelle Giglio Sebastian Duesing Venkat Malladi Ribo-seq Ribo-seq assay ribosomal profiling PMID:24468696 ribosomal profiling by sequencing assay Kasinathan et al., (February 2014). "High-resolution mapping of transcription factor binding sites on natitve chromatin." Nat Methods 11(2):203-9. doi: 10.1038/nmeth.2766. An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion. Chris Stoeckert Jie Zheng Venkat Malladi ATAC-seq ATAC-seq assay PMID:24097267 assay for transposase-accessible chromatin using sequencing Csorba et al., (November 2014). "Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization." Proc Natl Acad Sci 111(45):16160-5. doi: 10.1073/pnas.1419030111. A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing. Chris Stoeckert Jie Zheng Venkat Malladi ChIRP-seq ChIRP-seq assay Chromatin Isolation by RNA purification PMID:21963238 chromatin isolation by RNA purification sequencing assay Bohla et al., (September 2014). "A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking." PLoS One 9(9):e107765. doi: 10.1371/journal.pone.0107765. An assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA. Chris Stoeckert Jie Zheng Venkat Malladi STARR-seq STARR-seq assay self-transcribing active regulatory region sequencing PMID:23328393 self-transcribing active regulatory region sequencing assay Fudenberg et al., (November 2014). "High order chromatin architecture shapes the landscape of chromosomal alterations in cancer." Nat Biotechol 29(12):1109-13. doi: 10.1038/nbt.2049. A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture. Chris Stoeckert Jie Zheng Venkat Malladi Carbon-copy chromosome conformation capture assay followed by sequencing HiC HiC assay PMID:19815776 carbon-copy chromosome conformation capture assay followed by sequencing assay Protein-RNA interactions: new genomic technologies and perspectives. Nature Reviews Genetics 13 (2): 77-83. doi:10.1038/nrg3141 A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes. Chris Stoeckert Jie Zheng Venkat Malladi iCLIP iCLIP assay individual-nucleotide resolution cross-linking and immunoprecipitation doi:10.1016/j.ymeth.2013.10.011 individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay An assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs). Chris Stoeckert Jie Zheng Venkat Malladi RBNS RNA Bind-n-Seq RNBS assay doi: 10.1016/j.molcel.2014.04.016 RNA Bind-n-Seq assay Wu et al., (July 2014). "Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics. 2014 Jul 21;15:615. doi: 10.1186/1471-2164-15-615. A transcription profiling by RNA sequencing assay that quantitatively profiles RNA polyadenylation at the transcriptome level. Chris Stoeckert Jie Zheng Michelle Giglio Sebastian Duesing Venkat Malladi PAS-seq PAS-seq assay Poly(A)-site sequencing poly(A)-site sequencing assay doi: 10.1261/rna.2581711 polyA-site sequencing assay surface plasmon resonance sensor chip ProteOn GLC Sensor Chip #176-5011 A device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached Anna Maria Masci SPR sensor chip biosensor chip sensor chip OBI surface plasmon resonance sensor chip enzyme-linked antibody Goat anti-Mouse IgG-HRP (horse radish peroxidase) is an antibody linked to the enzyme horseradish peroxidase (HRP) that catalyzes the conversion of chromogenic substrates into colored products producing light when acting on chemiluminescent substrates (ECL). A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added. Bjoern Peters, Randi Vita, James A. Overton OBI enzyme-linked antibody A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. PERSON: Sagar Jain, Richard Scheuermann HiSeq 3000 http://www.illumina.com/systems/hiseq-3000-4000.html Illumina HiSeq 3000 A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. PERSON: Sagar Jain, Richard Scheuermann HiSeq 4000 http://www.illumina.com/systems/hiseq-3000-4000.html Illumina HiSeq 4000 A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a MHC:ligand complex. IEDB IEDB 3D structure|any method 3D molecular structure determination assay of a MHC:ligand complex An in vivo assay measuring B cell epitope specific protection from pathogen challenge using pathogen burden. IEDB IEDB pathogen burden after challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden An in vivo assay measuring B cell epitope specific protection from tumor challenge using tumor burden. IEDB IEDB tumor burden after challenge|in vivo assay in vivo assay measuring B cell epitope specific protection after tumor burden challenge A microarray assay that detects the binding of an antigen with an antibody. IEDB IEDB qualitative binding|microarray microarray assay measuring binding of a B cell epitope:antibody complex A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay. IEDB IEDB dissociation constant KD|nuclear magnetic resonance (NMR)|nM NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex A T cell epitope recognition assay that measures the immune response process resulting from the binding of a T cell receptor to epitope or the recongition of the epitope. IEDB IEDB biological activity|any method assay measuring biological activity resulting from T cell epitope:MHC:TCR binding A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells. IEDB IEDB CCL17/TARC release|biological activity assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells. IEDB IEDB MIF release|biological activity assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells. IEDB IEDB oncostatin M release|biological activity assay measuring epitope specific oncostatin M production by T cells A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant. IEDB IEDB binding constant|binding assay assay measuring a binding constant of a T cell epitope:MHC:TCR complex A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 17 production by T cells. IEDB IEDB CCL17/TARC release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells A cytometric bead array assay that detects chemokine (C-C motif) ligand 22 production by T cells. IEDB IEDB CCL22/MDC release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells An in vitro cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC. IEDB IEDB cytotoxicity|in vitro assay in vitro assay measuring epitope specific T cell killing A cytometric bead array assay that detects epitope specific granzyme A release by T cells. IEDB IEDB granzyme A release|cytometric bead array cytometric bead array assay measuring epitope specific granzyme A release by T cells A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme A release by T cells. IEDB IEDB granzyme A release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells A cytometric bead array assay that detects epitope specific granzyme B release by T cells. IEDB IEDB granzyme B release|cytometric bead array cytometric bead array assay measuring epitope specific granzyme B release by T cells A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme B release by T cells IEDB IEDB granzyme B release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells A cytometric bead array assay that detects macrophage migration inhibitory factor (MIF) production by T cells. IEDB IEDB MIF release|cytometric bead array cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells A cytometric bead array assay that detects oncostatin M production by T cells. IEDB IEDB oncostatin M release|cytometric bead array cytometric bead array assay measuring epitope specific oncostatin M production by T cells An enzyme-linked immunospot assay that detects epitope specific perforin release by T cells. IEDB IEDB perforin release|ELISPOT ELISPOT assay measuring epitope specific perforin release by T cells A T cell epitope specific proliferation assay that is performed in vivo. IEDB IEDB proliferation|in vivo assay in vivo assay measuring epitope specific proliferation of T cells A T cell epitope specific proliferation assay that is performed on cells in vitro. IEDB IEDB proliferation|in vitro assay in vitro assay measuring epitope specific proliferation of T cells An assay that detects the binding of a MHC molecule with a ligand, and produces a qualitative measurement of the binding as an output. IEDB IEDB qualitative binding|binding assay assay measuring qualitative binding of a MHC:ligand complex An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment. IEDB IEDB protection from challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from challenge T cell epitope dependent biological activity assay that detects suppression of an in vitro response. PERSON:Randi Vita, James Overton, Bjoern Peters IEDB suppression|in vitro assay assay measuring T cell epitope specific suppression in vitro An immune epitope assay that characterizes the structrue of a MHC-ligand complex, or detects the processing and presentation of a ligand by an antigen presenting cell, or the binding of a ligand to an MHC molecule. IEDB IEDB MHC ligand assay|any method MHC ligand assay collection of specimens Blood cells collected from multiple donors over the course of a study. A material entity that has two or more specimens as its parts. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens specimens derived from shared ancestor Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy. A collection of specimens derived from one common specimen via one or more material processing process(es). Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Chris Stoeckert, Jie Zheng specimen family Duke Biobank, OBIB, OBI Biobank specimens derived from shared ancestor specimen set collection process Collection of both blood and urine specimens in one clinical visit; Taking out liver and brain specimens during an autopsy. A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. Chris Stoeckert, Jie Zheng OBIB, OBI specimen set collection process specimens collected in one encounter Both blood and urine specimens collected in one clinical visit; liver and brain specimens taken during an autopsy. A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng specimen set OBIB, OBI Biobank specimens collected in one encounter human specimen set A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng Duke Biobank, OBIB, OBI Biobank human specimen set A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert Bjoern Peters, OBI specimens collected longitudinally An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest. Chris Stoeckert Paul D. Thomas reporter gene detection assay Paul D. Thomas, Yang Chai; FaceBase https://github.com/obi-ontology/obi/issues/781 reporter gene assay PMID 19268701: "we experimentally concatenated up to four enhancers from different genes and used a transgenic mouse assay to compare the in vivo activity of these compound elements with that of the single modules" A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest. Paul D. Thomas Yang Chai enhancer reporter gene assay FaceBase PMID 24614317 https://github.com/obi-ontology/obi/issues/781 enhancer activity detection by reporter gene assay PMID 19212405: "we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue" A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase. Paul D. Thomas Yang Chai chromatin modifier binding site identification by ChIP-Seq assay PMID:19212405 https://github.com/obi-ontology/obi/issues/782 transcription cofactor activity region identification by ChIP-Seq assay PMID 25977364: "Multiplexed imaging of mRNA expression using fluorescent hybridization chain reaction (HCR) quantitatively confirmed the expression profiles of lead cells" An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. Paul D. Thomas Yang Chai transcript expression location detection by fluorescent HCR. PMID:21037591 https://github.com/obi-ontology/obi/issues/783 transcript expression location detection by hybridization chain reaction assay A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected. Bjoern Peters Chris Stoeckert Jason Hilton OBI TAB-seq Tet-assisted bisulfite sequencing PMID:23196972 http://sourceforge.net/p/obi/obi-terms/789/ Tet-assisted bisulfite sequencing assay containing a specimen function A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay. For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ Chris Stoeckert Duke Biobank, OBIB Biobank containing a specimen function specimen container COPAN eSwab, CPT vacutainer, PAXgene Blood DNA tube A container with the function of containing a specimen. For details see tracker item: http://sourceforge.net/p/obi/obi-terms/792/ Chris Stoeckert Duke Biobank, OBIB specimen container container with environmental control a freezer. a humidity controlled box. A container with an environmental control function. For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/ Chris Stoeckert Duke Biobank, OBIB container with environmental control rapid amplification of cDNA ends A reverse transcribed polymerase chain reaction that is used to amplify a mRNA sequence between a defined internal site and the 5' or 3' end of the mRNA. For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ Jason Hilton, Chris Stoeckert RACE http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/RACE_Rapid_Amplification_of_cDNA_Ends/5_Prime_RACE_and_3_Prime_RACE ENCODE rapid amplification of cDNA ends 5' rapid amplification of cDNA ends A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 5' end of the mRNA. For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ Jason Hilton, Chris Stoeckert 5' RACE https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/5-race-system-for-rapid-amplification-of-cdna-ends.html ENCODE 5' rapid amplification of cDNA ends 3' rapid amplification of cDNA ends A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 3' end of the mRNA. For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ Jason Hilton, Chris Stoeckert 3' RACE https://www.thermofisher.com/us/en/home/references/protocols/nucleic-acid-amplification-and-expression-profiling/cdna-protocol/3-race-system-for-rapid-amplification-of-cdna-ends.html ENCODE 3' rapid amplification of cDNA ends 5' RNA ligase mediated rapid amplification of cDNA ends A 5' rapid amplification pf cDNA ends that uses RNA ligase to add an RNA adapter oligonucleotide to intact 5' mRNA ends, allowing the amplification of cDNA only from full-length, capped mRNA. For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/ Jason Hilton, Chris Stoeckert 5' RLM RACE https://tools.thermofisher.com/content/sfs/manuals/cms_056070.pdf ENCODE 5' RNA ligase mediated rapid amplification of cDNA ends MethylC-Capture Sequencing approach was introduced as a cost-effective and customizable alternative method for large-scale interrogation of functionally-active methylomes while simultaneously providing genetic variation information in a proof-of-concept epigenome-wide association study of 72 obese individuals, identifying novel disease-associated variants. A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing. Chris Stoeckert David Bujold Capture Methylome MCC-Seq MethylC-Capture Sequencing PMID:26021296 MethylC-Capture sequencing assay specimen family creation Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections, processing blood into buffy coat, red cells, and serum. A material processing that has as its input a specimen and as its output a collection of specimens. For details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Mathias Brochhausen, Chris Stoeckert, Jie Zheng OBI, OBIB Biobank specimen family creation A CFSE assay that detects T cell epitope specific proliferation in vitro. IEDB IEDB proliferation|CFSE carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells A T cell epitope binding constant determination assay that measures the dissociation constant KD. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB dissociation constant KD|binding assay|nM assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex A T cell epitope binding constant determination assay that measures the on rate. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB on rate|binding assay|M^-1s^-1 assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex A T cell epitope binding constant determination assay that measures the off rate. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB off rate|binding assay|1/s assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex A T cell epitope binding constant determination assay that measures the association constant KA. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB association constant KA|binding assay|1/nM assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex A small-angle scattering 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB 3D structure|small-angle scattering assay small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex A bio-layer interferometry assay that measures the on rate of an antigen with an antibody. IEDB IEDB on rate|bio-layer interferometry assay|M^-1s^-1 bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex A bio-layer interferometry assay that measures the off rate of an antigen with an antibody. IEDB IEDB off rate|bio-layer interferometry assay|1/s bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex A bio-layer interferometry assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB qualitative binding|bio-layer interferometry assay bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex A bio-layer interferometry assay that measures the dissociation constant [KD] of an antigen with an antibody. IEDB IEDB dissociation constant KD|bio-layer interferometry assay|nM bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division. An assay using carboxyfluorescein succinimidyl ester staining. IEDB CFSE assay IEDB carboxyfluorescein succinimidyl ester staining assay Detecting the presence of an antibody in a cell culture supernatant by detecting a shift in the interference pattern reflected from a layer of immobilized protein to which the antibody binds. A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor. IEDB biolayer interferometry, BLI IEDB bio-layer interferometry assay Targeting a solution of antibody bound to a protein with a neutron beam to determine the binding site of the antibody on the protein A 3D molecular structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined. IEDB SAXS IEDB small-angle scattering 3D molecular structure determination assay A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features. Term request: https://sourceforge.net/p/obi/obi-terms/791/ Jason Hilton, Chris Stoeckert, Bjoern Peters, OBI-group NimbleGen Human 6x630K CGH Whole Genome Tiling Array http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=snolquwezzwdxuj&acc=GPL18318 Human 6x630K CGH Whole Genome Tiling Array The doi symbol: "10.1109/5.771073" resolves to ieee website: http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=771073 A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles. Discussed on Aug 22, 2016 OBI dev call. Details see tracker: https://sourceforge.net/p/obi/obi-terms/818/ OBI developers DOI https://en.wikipedia.org/wiki/Digital_object_identifier https://www.doi.org/ digital object identifier An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments. Chris Stoeckert Jason Hilton eCLIP PMID:27018577 enhanced cross-linking immunoprecipitation high-throughput sequencing assay A transcription profiling by RNA sequencing assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits. Chris Stoeckert Jason Hilton Mark A. Miller Michelle Giglio Sebastian Duesing short RNA-seq small RNA-seq url:http://science.sciencemag.org/content/316/5830/1484.full url:http://www.illumina.com/techniques/sequencing/rna-sequencing/small-rna-seq.html https://github.com/obi-ontology/obi/issues/859 small RNA sequencing assay A transcription profiling by RNA sequencing assay used to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs. Chris Stoeckert Jason Hilton Michelle Giglio Sebastian Duesing Bru-seq PMC:4009065 bromouridine labeling and sequencing assay A transcription profiling by RNA sequencing assay used to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time. Chris Stoeckert Jason Hilton Michelle Giglio Sebastian Duesing BruChase-seq PMC:4009065 bromouridine pulse-chase and sequencing assay Whole human blood samples were incubated with lipopolysaccharide (LPS) to examine dose-dependent signaling responses within the toll-like receptor 4 (TLR4) pathway. After LPS stimulation, rare earth metal tagged antibodies against phenotypic markers were used to stain the blood sample (Nd143-CD45RA, Nd145-CD4, Er170-CD3, Sm152-TCR__, Pr141-CD7, Nd146-CD8, Nd142-CD19). A Fluidigm CyTOF version 1 instrument equipped with CyTOF software version 5.1.648 was used to measure and analyze the levels of antibody staining reflective of the level of expression of those surface receptors. A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry. ImmPort CyTOF mass cytometry assay PMID:26190063 cytometry time of flight assay On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml. An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution. ImmPort HPLC PMID:9491555 high performance liquid chromatography assay WGS permits comprehensive sequencing of introns and exons, whereas whole exome sequencing (WES) allows deeper sequencing of exonic regions at a lower cost. Due to the large number of genetic variants found in each genome, it is necessary to use filtering approaches to distinguish deleterious from benign variants. WES has been used successfully to identify novel genetic causes of primary immunodeficiency. Complex structural variations and non-Mendelian disorders remain challenges for WGS. A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism. Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. ImmPort WGS PMID:23095910 PMID:25827230 whole genome sequencing assay DNA was extracted from the Ficoll pellet of blood taken from congenital asplenia patients. Unamplified, high-molecular weight, RNase-treated genomic DNA (4_6 _g) was used for whole exome sequencing (WES) with the use of Agilent 71 Mb (V4 + UTR) singlesample capture and an Illumina HiSeq 2000. Sequencing was carried out so as to obtain 30_ coverage from 2 _ 100-bp paired-end reads. We used the Annovar tool (25) to annotate the resulting highquality (HQ) variants. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and13,325, respectively. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called. A mean of 105 coding HQ SNVs and 32 indels was identified. A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons). ImmPort WES PMID:25827230 exome sequencing assay Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy. An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye. ImmPort PMID:21685355 microscopy assay T cells were separated from PBL of laboratory volunteers and used as responder cells (R). Mitomycin C-treated allogeneic mAPC enriched populations were used as stimulators (S), incubated for 5 days, pulsed with 3H-thymidine (3H-TdR) for 16 hours, harvested, and radioactivity counted using a beta scintillation counter to measure proliferation of the 3H-thymidine labeled cells. A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators). ImmPort MLR PMID:14969764 mixed lymphocyte reaction assay DNA was isolated from PBMCs from healthy donors.The single-nucleotide polymorphism (SNP) assay was performed on an HT7900 Sequence Detection System (Applied Biosystems) following the allelic discrimination assay protocol provided by the manufacturer. Primers for the assay were designed in such a way that they amplified all the alleles of a particular HLA type (HLA-B or HLA-C) as well as the amplicon containing the polymorphic region of interest. Two probes were designed with a single mismatch between them. Each probe bound only one group of alleles and was labeled with either 6FAM or VIC fluorescent dye at its 5_ end. The 3_ end of the probes contained a quencher. For KIR2DL1 functional allele typing, the probe was designed based on a single-nucleotide mismatch at amino acid position 245 in the mature protein. A universal primer was designed that could specifically amplify all the alleles of KIR2DL1.The SNP assay was run on the HT7900 using the same protocol as described for KIR ligand typing. Results showed that 20 individuals had only arginine at amino acid position 245 of KIR2DL1, 5 were heterozygous for arginine and cysteine, and 1 had only cysteine in that position.Thus, this approach was useful not only for the identification of functional groups of KIR alleles, but also for determining the presence of the KIR gene itself. A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined. Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. ImmPort KIR typing PMID:21239231 killer cell immunoglobulin-like receptor typing assay Blood samples from Holstein-Friesian heifer calves were used to isolate white blood cell (WBC) pellets, from which total RNA was extracted using Tri-reagent and cDNA generated using a Reverse Transcription Kit, both_ according to the manufacturers? instructions. An alignment of sequences of known bovine MHCI gene cDNAs, as presented in the IPD-MHC database (May 2014), was used to design a series of 3_ (for) and 5_ (rev) pan-MHCI primers. cDNA from individual animals was subject to PCR amplification in two separate reactions using either the For1/Rev2 or the For3/Rev1 primer pairs. For each sample primers using a unique combination of MID tags were used to allow subsequent de-multiplexing of the sequence data. PCRs were conducted using the Phusion High-Fidelity PCR kit. Following amplification, 5?_l of PCR products from each sample were pooled, purified using Agencourt AMPure XP Beads and run on a 1.5?% agarose gel. Bands of the appropriate size_ were extracted and purified using the Qiagen Gel extraction kit. Libraries were submitted to Edinburgh Genomics where after standard quality control procedures they underwent 300 base paired-end sequencing on an Illumina MiSeq v3. Data were separated into reads generated from For1Rev2 and For3Rev1 primer pairs, generating separate datasets for up to 192 samples. Within each sample, reads were clustered into unique variants which were subsequently compared using BLAST against a database of the previously identified bovine MHCI sequences. This process identified >140 novel classical MHCI genes and defined 62 novel MHCI haplotypes, dramatically expanding the known bovine MHCI repertoire. A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined. Genotyping assays should ideally identify which part of the genome the information is about. We do not currently have a good way to do this. That information should be added later. IEDB MHC typing, HLA typing PMC:2628004 PMID:27516207 major histocompatibility typing assay IHC slide staining A staining using labeled antibodies, i.e. the analytical part of immunohistochemistry. The staining is applied to fixed specimens on slides to identify biomarkers in tissues. Chris Stoeckert, Ned Haubein http://www.agilent.com/cs/library/technicaloverviews/public/08002_ihc_staining_methods.pdf IHC slide staining H&E slide staining A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink. Chris Stoeckert, Ned Haubein http://www.histalim.com/accueil/activities/our-services/histology/hematoxylin-eosin-2/ H&E slide staining H&E-stained fixed tissue slide specimen A fixed tissue slide specimen that is the output of H&E slide staining. Chris Stoeckert, Ned Haubein OBIB, OBI H&E-stained fixed tissue slide specimen IHC-stained fixed tissue slide specimen A fixed tissue slide specimen that is the output of immunohistochemistry slide staining. Chris Stoeckert, Ned Haubein OBIB, OBI IHC-stained fixed tissue slide specimen A cell specimen that contains only one cell. Requested by Sirarat Sarntivijai (EBI). Details see tracker: https://sourceforge.net/p/obi/obi-terms/828/ PERSON: Jie Zheng, Alexander Diehl PERSON: Jie Zheng, Alexander Diehl single cell specimen Illumina Genome Analyzer A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run. Person: Chris Stoeckert, Jason Hilton Illumina Genome Analyzer I http://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html Illumina Genome Analyzer Illumina HiSeq X Ten A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. Person: Chris Stoeckert, Jason Hilton, Sagar Jain, Richard Scheuermann HiSeq X Ten http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html Illumina HiSeq X Ten Illumina Infinium Omni5Exome-4 Kit An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation. Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html Illumina Infinium Omni5Exome-4 Kit Illumina Infinium MethylationEPIC v1.0 BeadChip An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution. Person: Chris Stoeckert, Jason Hilton http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf Illumina Infinium MethylationEPIC v1.0 BeadChip An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based proteomics is used to analyze the time-dependent decay and determine protein stability. Rob Nash dynamic SILAC pulse SILAC pulsed SILAC PMID:18954100 PMID:19053139 pulse stable isotope labeling by amino acids in cell culture A cytometric bead array assay that detects chemokine (C-C motif) ligand 20 production by T cells. PERSON:Randi Vita, James Overton, Bjoern Peters IEDB CCL20/MIP-3a release|cytometric bead array cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 20 production by T cells. PERSON:Randi Vita, James Overton, Bjoern Peters IEDB CCL20/MIP-3a release|biological activity assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells RNA Integrity Number calculation A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace. Chris Stoeckert, Bjoern Peters RIN calculation https://www.agilent.com/cs/library/applications/5989-1165EN.pdf RNA Integrity Number calculation RNA Integrity Number value specification A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact). Chris Stoeckert, Bjoern Peters RIN value specification OBI RNA Integrity Number value specification temperature value specification A value specification that specifies the temperature of some thing. Chris Stoeckert OBI temperature value specification volume value specification A value specification that specifies the volume of some thing. Chris Stoeckert OBI volume value specification An assay to determine the temperature of an evaluant. Bjoern Peters Chris Stoeckert OBI temperature measurement assay An assay to determine the volume of an evaluant. Bjoern Peters Chris Stoeckert OBI volume measurement assay A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification. Chris Stoeckert Jason Hilton microRNA counts PMID:26729350 url:http://www.nanostring.com/applications/technology https://github.com/obi-ontology/obi/issues/806 ENCODE DCC Nanostring nCounter miRNA expression assay A transcription profiling by RNA sequencing assay used to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions. Chris Stoeckert Jason Hilton Michelle Giglio Sebastian Duesing BruUV-seq PMC:4675984 https://github.com/obi-ontology/obi/issues/827 ENCODE DCC bromouride labeling and sequencing after UV exposure An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods. Chris Stoeckert Jason Hilton circulome-seq eccDNA-seq url:http://biorxiv.org/content/early/2017/04/19/128686 https://github.com/obi-ontology/obi/issues/830 ENCODE DCC extrachromosomal circular DNA sequencing assay Test performed using antibodies produced by human B-cells that bind with human immunodeficiency virus (HIV) antigens An analyte assay that measures the presence or amount of antibodies to a specified antigen. Bjoern Peters Chris Stoeckert James Overton Randi Vita OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB antigen specific antibodies assay An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens. HIV-1 and HIV-2 are two different viruses (http://i-base.info/qa/36) Bjoern Peters Chris Stoeckert James Overton Randi Vita HIV I/II Ab assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB HIV antibody assay An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens. https://www.cdc.gov/mmwr/preview/mmwrhtml/00042810.htm Bjoern Peters Chris Stoeckert James Overton Randi Vita HIV I/II Plus O assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB HIV group O antibody assay An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens. Bjoern Peters Chris Stoeckert James Overton Randi Vita HBsAb assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB surface HBV antibody assay An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens. Bjoern Peters Chris Stoeckert James Overton Randi Vita HBcAb assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB core HBV antibody assay An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens. Bjoern Peters Chris Stoeckert James Overton Randi Vita HBcAb-IgM assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB core HBV IgM antibody assay An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens. Bjoern Peters Chris Stoeckert James Overton Randi Vita HCV Ab assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB HCV antibody assay An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens. Bjoern Peters Chris Stoeckert James Overton Randi Vita EBV IgG Ab assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB EBV IgG antibody assay An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens. Bjoern Peters Chris Stoeckert James Overton Randi Vita EBV IgM Ab assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB EBV IgM antibody assay An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens. Bjoern Peters Chris Stoeckert James Overton Randi Vita CMV Ab assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB CMV antibody assay An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood. Bjoern Peters Chris Stoeckert James Overton Randi Vita VDRL test OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB venereal disease research laboratory test An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope. Bjoern Peters Chris Stoeckert James Overton Randi Vita RPR assay url:http://www.differencebetween.net/science/health/difference-between-vdlr-and-rpr/ https://github.com/obi-ontology/obi/issues/825 NCI BBRB rapid plasma reagin test An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens. Bjoern Peters Chris Stoeckert James Overton Randi Vita HBsAg assay OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB HBV surface antigen assay An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids. Bjoern Peters Chris Stoeckert James Overton Randi Vita HIV-1 NAT OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB HIV-1 nucleic acid testing An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids. Bjoern Peters Chris Stoeckert James Overton Randi Vita HCV NAT OBI https://github.com/obi-ontology/obi/issues/825 NCI BBRB HCV nucleic acid testing A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states. Chris Stoeckert Jason Hilton Mint-ChIP Mint-ChIP-seq url:http://www.cell.com/molecular-cell/abstract/S1097-2765(15)00863-1 https://github.com/obi-ontology/obi/issues/829 ENCODE DCC multiplexed indexed T7 ChIP-seq assay A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._ Rebecca Jackson SELEX PMID:21720957 systematic evolution of ligands by exponential enrichment assay An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions. Bjoern Peters doi:10.1002/3527600906.mcb.200300025 footprinting assay An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis Rebecca Jackson OBI development call DNAse footprinting assay A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together. Rebecca Jackson ECO:0001095 PMID:9043710 mammalian 2-hybrid assay An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied. Rebecca Jackson OBI development call protein localization assay A protein localization assay that determines the specific location of a protein in a living tissue sample. Rebecca Jackson PMID:14686950 tissue-based protein localization assay A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy. Rebecca Jackson ECO subcellular protein localization assay An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins. Rebecca Jackson ECO subcellular protein immunohistochemistry assay A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples. Chris Stoeckert PMID:18388953 ChIP-qPCR assay A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules. Chris Stoeckert PMID:20541015 genomic SELEX An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies. Bjoern Peters dot blot analysis PMID:10473518 dot blot assay A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane. Bjoern Peters Northwestern analysis Northwestern assay PMID:26965261 Northwestern blot assay A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane. Bjoern Peters PMID:26404144 Southwestern blot assay An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed Bjoern Peters immunocytochemistry An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen. Rebecca Jackson ATP quantitation assay cell viability ATP quantitation assay ECO ATP bioluminescence assay An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance). Note that electrophysiological manipulations also exist which involve processes that alter the electrophysiological properties of cells and tissues. Gully Burns url:https://en.wikipedia.org/wiki/Electrophysiology electrophysiology assay An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations. Gully Burns ECO:0006012 url:http://www.annualreviews.org/doi/pdf/10.1146/annurev.ph.46.030184.002323 url:https://en.wikipedia.org/wiki/Patch_clamp patch clamp assay A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. Gully Burns ECO:0006015 url:https://en.wikipedia.org/wiki/Patch_clamp#Whole-cell_recording_or_whole-cell_patch whole-cell patch clamp assay A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell. Gully Burns url:https://en.wikipedia.org/wiki/Patch_clamp#Cell-attached_patch cell-attached patch clamp assay A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations. Gully Burns url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ url:https://en.wikipedia.org/wiki/Patch_clamp#Inside-out_patch inside-out patch clamp assay A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels. Gully Burns url:http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ url:https://en.wikipedia.org/wiki/Patch_clamp#Outside-out_patch outside-out patch clamp assay An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell. Gully Burns url:https://en.wikipedia.org/wiki/Voltage_clamp voltage clamp assay The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation. Gully Burns TEVC url:https://en.wikipedia.org/wiki/Voltage_clamp#Two-electrode_voltage_clamp_using_microelectrodes two electrode voltage clamp assay The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques. Gully Burns COVG PMID:9711615 cut open oocyte voltage clamp assay The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels. Gully Burns url:https://en.wikipedia.org/wiki/Electrophysiology#Current_clamp current clamp assay An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface. Gully Burns EEG electroencephalography An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique. Can be used on any cell, not just neurons. Gully Burns url:http://www.thieme.com/media/samples/pubid-80418214.pdf single-unit recording An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time. Gully Burns multi-unit recording An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue. Gully Burns doi:10.1007/978-1-4614-7320-6_723-1 local field potential recording courier organization An organization that delivers messages, packages, and mail. Chris Stoeckert, Helena Ellis courier https://en.wikipedia.org/wiki/Courier NCI BBRB courier organization courier tracking number A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item. Chris Stoeckert, Helena Ellis OBIB NCI BBRB courier tracking number Leica Peloris rapid tissue processor An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories. Chris Stoeckert, Helena Ellis http://drp8p5tqcb2p5.cloudfront.net/fileadmin/downloads_lbs/Leica%20PELORIS/User%20Manuals/Leica_Peloris_manual_EN.pdf NCI BBRB Leica Peloris rapid tissue processor Microm Ergostar HM200 A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right. Chris Stoeckert, Helena Ellis http://www.ultra-medical.com/Microm-Ergostar-HM200-Microtome/en NCI BBRB Microm Ergostar HM200 microtome blade A device that is the part of a microtome used to slice specimens to a desired thickness. Chris Stoeckert, Helena Ellis https://en.wikipedia.org/wiki/Microtome NCI BBRB microtome blade Sakura Low profile Accu-Edge microtome blade A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering. Chris Stoeckert, Helena Ellis http://www.sakura.eu/Our-products/item/8/Microtomy/29/Accu-Edge-Disposable-Microtome-Blades NCI BBRB Sakura Low profile Accu-Edge microtome blade tissue section thickness A length measurement datum that is the result of an assay measuring the thickness of a tissue section. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB tissue section thickness molecular analysis facility organization An analysis facility that includes analysis of molecular metabolites, as well as the various DNAs and RNAs. An organization that provides molecular analysis service. Chris Stoeckert, Helena Ellis MAF NCI BBRB, OBIB NCI BBRB molecular analysis facility organization cannot be assessed, not applicable, unknown An information content entity that provides an explanation why a data item is not provided. Chris Stoeckert, Helena Ellis OBI NCI BBRB reason for lack of data item A reason for lack of data item that is the negative output of a determination if assay will provide reliable results. Chris Stoeckert, Helena Ellis cannot be assessed OBI NCI BBRB cannot be assessed determination A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay. Chris Stoeckert, Helena Ellis OBI NCI BBRB determination if assay will provide reliable results AJCC 7th edition GX: cannot be assessed. A cannot be assessed determination for histologic tumor grade. Chris Stoeckert, Helena Ellis OBI NCI BBRB GX AJCC 7th edition pTX: cannot be assessed. A cannot be assessed determination for pathologic primary tumor staging. Chris Stoeckert, Helena Ellis OBI NCI BBRB pTX AJCC 7th edition pNX: cannot be assessed. A cannot be assessed determination of pathologic staging of lymph nodes. Chris Stoeckert, Helena Ellis OBI NCI BBRB pNX G1:Well differentiated G4: Undifferentiated A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade according to AJCC 7th edition A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Chris Stoeckert, Helena Ellis Histologic Grade (Fuhrman Nuclear Grading System) NCI BBRB, OBI NCI BBRB histologic grade according to the Fuhrman Nuclear Grading System A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to a two-tier grading system A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to the World Health Organization A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread lung primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: colon distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for colon according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: lung distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: kidney distant Metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: ovarian distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for ovary according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. Chris Stoeckert, Helena Ellis Clinical tumor stage group (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB clinical tumor stage group according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. Chris Stoeckert, Helena Ellis Clinical FIGO stage NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics cervical cancer stage value specification A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. Chris Stoeckert, Helena Ellis Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics ovarian cancer stage value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis Performance Status Scale https://en.wikipedia.org/wiki/Performance_status NCI BBRB performance status value specification A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. Chris Stoeckert, Helena Ellis ECOG score NCI BBRB, OBI NCI BBRB Eastern Cooperative Oncology Group score value specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky Score NCI BBRB, OBI NCI BBRB Karnofsky score vaue specification A clinical history in which there is a diagnosis of cancer. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB clinical history of cancer A clinical history in which there was no diagnosis of cancer. Chris Stoeckert, Helena Ellis clinical history of no cancer NCI BBRB, OBIB NCI BBRB clinical history devoid of cancer A clinical history in which it is not known whether there was a diagnosis of cancer. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB unknown clinical history of cancer A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer. Chris Stoeckert, Helena Ellis cancer diagnosis OBIB NCI BBRB diagnosis of cancer A clinical history in which there is a diagnosis of cancer in a blood relative. Chris Stoeckert, Helena Ellis family history of cancer NCI BBRB, OBIB NCI BBRB family clinical history of cancer A clinical history in which there is a diagnosis of cancer in the female sibling of a parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB aunt clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male sibling. Chris Stoeckert, Helena Ellis OBIB NCI BBRB brother clinical history of cancer A clinical history in which there is a diagnosis of cancer in a person's female child. Chris Stoeckert, Helena Ellis OBIB NCI BBRB daughter clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB father clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB mother clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female sibling. Chris Stoeckert, Helena Ellis OBIB NCI BBRB sister clinical history of cancer A clinical history in which there is a diagnosis of cancer in a person's male child. Chris Stoeckert, Helena Ellis OBIB NCI BBRB son clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male sibling of a parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB uncle clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female parent of a parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB grandmother clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male parent of a parent. Chris Stoeckert, Helena Ellis OBIB NCI BBRB grandfather clinical history of cancer A clinical history in which there is a diagnosis of cancer in a male child of a sibling. Chris Stoeckert, Helena Ellis OBIB NCI BBRB nephew clinical history of cancer A clinical history in which there is a diagnosis of cancer in a female child of a sibling. Chris Stoeckert, Helena Ellis OBIB NCI BBRB niece clinical history of cancer A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease. Chris Stoeckert, Helena Ellis OBIB NCI BBRB diagnosis of infectious disease A diagnosis of infectious disease caused by the hepatitis B virus. Chris Stoeckert, Helena Ellis OBIB NCI BBRB diagnosis of hepatitis B A diagnosis of infectious disease caused by the hepatitis C virus. Chris Stoeckert, Helena Ellis OBIB NCI BBRB diagnosis of hepatitis C A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2). Chris Stoeckert, Helena Ellis OBIB NCI BBRB diagnosis of HIV A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB clinical history of repeated HIV assays A clinical history in which there has been second hand exposure to tobacco smoking. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB exposure to second hand smoke An exposure to second hand smoke that occurred in the (patient's) household when the person was a child. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB exposure to second hand smoke in household during childhood An exposure to second hand smoke in person's current household. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB exposure to second hand smoke in current household A clinical history in which a female has had a pregnancy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB pregnancy history A measurement datum of the total number of pregnancies a woman has had. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB number of pregnancies A measurement datum of the total number of live births a female has had. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB number of live births An age measurement datum performed on a female when her first biological child was born. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB age when gave birth to first child A clinical history in which a woman has had gynecologic surgery in the past. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB gynecologic surgery history A gynecologic surgery history in which a woman has had a hysterectomy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB hysterectomy history A gynecologic surgery history in which a woman has had a unilateral oophorectomy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB unilateral oophorectomy history A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB neither hysterectomy nor oophorectomy history An information content entity that indicates whether a woman has ever used oral contraceptives in order to block ovulation and prevent the occurrence of pregnancy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB hormonal birth control use history A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB hormonal birth control former use history A hormonal birth control use history that indicates an individual is currently a hormonal birth control user. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB hormonal birth control current use history A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB no hormonal birth control use history A clinical history in which an individual has had hormonal replacement therapy in the past. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB hormonal replacement therapy history A processed material used for delivery of hormones in hormone replacement therapy. Chris Stoeckert, Helena Ellis form of hormone replacement therapy NCI BBRB, OBIB NCI BBRB delivery form for hormonal replacement therapy A delivery form for hormonal replacement therapy that is a pill for oral administration. Chris Stoeckert, Helena Ellis OBIB NCI BBRB pill delivery form for hormonal replacement therapy A delivery form for hormonal replacement therapy that is a patch for transdermal administration. Chris Stoeckert, Helena Ellis OBIB NCI BBRB patch delivery form for hormonal replacement therapy A delivery form for hormonal replacement therapy that is a cream for transdermal administration. Chris Stoeckert, Helena Ellis OBIB NCI BBRB cream delivery form for hormonal replacement therapy An information content entity that indicates the state of a female's cessation of menstruation. Chris Stoeckert, Helena Ellis OBIB NCI BBRB menopausal status A menopausal status that is neither pre- nor post-menopausal. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB indeterminate menopausal status A menopausal status indicating that less than 6 months has passed since the last menstrual period and there has not been prior bilateral oophorectomy and not on estrogen replacement. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB premenopausal status A menopausal status indicating that it has been 6-12 months since last menstrual period. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB perimenopausal status A menopausal status indicating that it has been more than 12 months since the last menstrual period with no prior hysterectomy or that there has been a prior bilateral oophorectomy. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB postmenopausal status An information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment. Chris Stoeckert, Helena Ellis OBIB NCI BBRB exposure to environmental and workplace carcinogens history An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic. Chris Stoeckert, Helena Ellis OBIB NCI BBRB exposure to arsenic history An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos. Chris Stoeckert, Helena Ellis OBIB NCI BBRB exposure to asbestos history An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust. Chris Stoeckert, Helena Ellis OBIB NCI BBRB exposure to diesel exhaust history An exposure to environmental and workplace carcinogens history where the carcinogen is chromium. Chris Stoeckert, Helena Ellis OBIB NCI BBRB exposure to chromium history An exposure to environmental and workplace carcinogens history where the carcinogen is silica. Chris Stoeckert, Helena Ellis OBIB NCI BBRB exposure to silica history An information content entity that indicates whether or not an entity has met a specific requirement in order to take part in a given process. Chris Stoeckert, Helena Ellis eligibility criterion met NCI BBRB, OBIB NCI BBRB indicator of whether an inclusion criterion was met An information content entity that indicates whether or not an entity has met all specific requirements in order to take part in a given process. Chris Stoeckert, Helena Ellis all eligibility criteria met NCI BBRB, OBIB NCI BBRB indicator of whether all inclusion criteria were met An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB age of majority inclusion criterion An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB chemotherapy treatment exclusion criterion An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB radiation treatment exclusion criteria An exclusion criterion defined by the pathologist is defined as whether the individual received chemotherapy within the last two years. An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB chemotherapy treatment within the recent past exclusion criterion An exclusion criterion defined by the pathologist is defined as whether the individual received radiation therapy within the last two years. An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB radiation treatment within the recent past exclusion criterion An important inclusion criterion is for for the individual to have a BMI between 18.5 and 35.0 An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB BMI range inclusion criterion An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within 48 hours prior to death. An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB blood transfusion exclusion criterion An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB history of metastatic cancer exclusion criterion Donor eligibility based on history of intravenous drug abuse in the last 5 years. An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB intravenous drug use exclusion criterion Donor eligibility based on whether the donor has a history of sex with someone who has been diagnosed or at risk for HIV/AIDS and/or HCV and/or HBV in the last 5 years. An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB history of sex with someone with a history of blood borne infection exclusion criterion Donor eligibility based on whether the donor has a history of sex with someone who has used intravenous drugs in the last 5 years. An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB history of sex with someone with a history of intravenous drugs exclusion criterion An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB HIV exclusion criterion Donor eligibility based on whether the donor has been exposed to HIV/AIDS. An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process. Chris Stoeckert, Helena Ellis NCI BBRB, OBIB NCI BBRB exposure to blood borne infectious disease exclusion criterion An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry. Rebecca Jackson PMID:26463381 RNA interactome capture A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated. Jie Zheng WFM url:http://bitesizebio.com/19409/the-many-flavors-of-widefield-microscopy/ url:https://svi.nl/WideFieldMicroscope widefield microscopy assay An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei. Chris S PMID:8327891 nuclear ligation assay A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR. Chris S 3C assay PMID:11847345 url:http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.243.html chromosome conformation capture assay A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes. Chris S PMID:20461051 Hi-C assay An assay that produces a description of the qualities of an organism that has not been transformed, through observation and physical, non-invasive techniques. physical examination of an organism A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site. Jie Zheng PMID:21770468 hydroxyl-radical footprinting assay A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA. Jie Zheng MPE-Fe(II) footprinting PMID:6225070 PMID:6435669 methidiumpropyl-EDTA-iron(II) footprinting assay A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role. Person: Alan Ruttenberg, Jie Zheng https://en.wiktionary.org/wiki/measurand https://github.com/obi-ontology/obi/issues/778 measurand role A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached. Rebecca Jackson PMID:23378648 url:https://en.wikipedia.org/wiki/Primer_extension transcription start site mapping by primer extension assay A study design in which proteins in a sample are detected, quantified or otherwise analysed. Dan Berrios OBI:0001441 proteomic profiling design An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library. Rebecca Jackson SSH subtractive hybridization PMID:14970460 suppression subtractive hybridization An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes. Rebecca Jackson DSH differential screening PMID:25472628 differential screening hybridization A footprinting assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, James Overton, Bjoern Peters IEDB qualitative binding|footprinting assay footprinting assay measuring binding of a B cell epitope:antibody complex A hydroxyl-radical footprinting assay that detects the binding of an antigen with an antibody. PERSON:Randi Vita, James Overton, Bjoern Peters IEDB qualitative binding|hydroxyl-radical footprinting assay hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex An enzyme-linked immunosorbent assay that detects interferon-alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNa release|ELISA ELISA measuring epitope specific interferon-alpha production by T cells A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IFNa release|biological activity assay measuring epitope specific interferon-alpha production by T cells ‘diagnosed with Type 2 diabetes mellitus’, ‘E11.4’, ’not finding of hypertension' An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process. Mathias Brochhausen MIABIS2.0 health status inclusion criterion 'smoking behavior’ An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process. Mathias Brochhausen MIABIS2.0 clinically relevant lifestyle inclusion criterion 'exposure to cigarette smoke’, ‘exposure to lead through drinking water' An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process. Mathias Brochhausen MIABIS2.0 clinically relevant exposure inclusion criterion 'pregnant’, ‘not pregnant' An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process. Mathias Brochhausen MIABIS2.0 gravidity inclusion criterion A transcription profiling by RNA sequencing assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends. Michelle Giglio Rebecca Jackson Sebastian Duesing PRO-Seq precision nuclear run-on and sequencing assay PMID:23430654 https://github.com/obi-ontology/obi/issues/876 precision nuclear run-on sequencing assay A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. Rebecca Jackson 4C assay circularized chromosome conformation capture assay url:http://www.sciencedirect.com/science/article/pii/B9780123919380000045 https://github.com/obi-ontology/obi/issues/875 chromosome conformation capture-on-chip assay A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples. Rebecca Jackson haplotype reconstruction by Hi-C assay PMID:19815776 url:https://www.nature.com/articles/nbt.2728 https://github.com/obi-ontology/obi/issues/828 genotype phasing by Hi-C assay defined population inclusion criterion inclusion based on age, sex, and living region (rural area or specified city). An inclusion criterion that is based on fitting within the defined characteristics of a population based study design. Chris Stoeckert, Mathias Brochhausen MIABIS 2.0 https://github.com/obi-ontology/obi/issues/920 MIABIS 2.0 defined population inclusion criterion BCL format A data format specification that is a binary file containing base calling data. These files are created by sequencing machines during the act of sequencing, and contain data about each of the nucleotide clusters on a sequencing flow cell. Stephen A. Fisher, Junhyong Kim, Dan Berrios BCL format ERCC RNA spike-in A processed material developed by the External RNA Controls Consortium (ERCC) that consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids. Stephen A. Fisher, Junhyong Kim, Dan Berrios https://www.thermofisher.com/order/catalog/product/4456740 ERCC RNA spike-in SIRV RNA spike-in A processed material that consists of transcript isoforms of 7 spike-in RNA variant (SIRV) genes and possibly the 92 External RNA Controls Consortium (ERCC) RNA spike-in genes. Stephen A. Fisher, Junhyong Kim, Dan Berrios https://www.lexogen.com/sirvs/design/ SIRV RNA spike-in SRS identifier An accession number that applies to a database record for an individual sample object in an NCBI Sequence Read Archive (SRA) submission. These records are imported from the NCBI BioSample database. Stephen Fisher, Dan Berrios SRA sample accession number SRS identifier age since culture seeding measurement datum An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish). Stephen A. Fisher, Junhyong Kim, Dan Berrios age of culture age since culture seeding measurement datum alignment counting algorithm An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts). Stephen A. Fisher, Junhyong Kim, Dan Berrios alignment counting algorithm alignment counting application A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes. Stephen A. Fisher, Junhyong Kim, Dan Berrios doi:10.1093/bioinformatics/btu638 alignment counting application base calling algorithm An algorithm that assigns nucleotides to temporal or spatial peaks generated by a detector, such as peaks of light intensities generated by a DNA sequencer Stephen A. Fisher, Junhyong Kim, Dan Berrios base calling algorithm base calling application A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis. Stephen A. Fisher, Junhyong Kim, Dan Berrios base calling application bcl2fastq software application A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. Stephen A. Fisher, Junhyong Kim, Dan Berrios https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html bcl2fastq software application date process started A data item that is the date when a process was initiated. Chris Stoeckert, Daniel Berrios, Stephen A. Fisher date process started dbGaP study identifier A central registered identifier symbol that denotes a specific study in dbGaP. Stephen A. Fisher, Junhyong Kim, Dan Berrios dbGaP accession number doi:10.1038/ng1007-1181 dbGaP study identifier material amplification role A worker role played by the person who runs the enzymatic amplifying process. Stephen A. Fisher, Junhyong Kim, Dan Berrios material amplification role material sequencing library preparation role A worker role played by the person who performs the library preparation process to generate a sequencing library for a sample to be sequenced. Stephen A. Fisher, Junhyong Kim, Dan Berrios material sequencing library preparation role number of PCR cycles during library construction A data item that is the number of PCR cycles used during the construction of a sequencing library. Stephen A. Fisher, Junhyong Kim, Dan Berrios library construction PCR cycles https://en.wikipedia.org/wiki/Polymerase_chain_reaction number of PCR cycles during library construction number of rounds of amplification A data item that is the number of times an amplification reaction happened. Stephen A. Fisher, Junhyong Kim, Dan Berrios number of rounds of amplification reference genome role A reference substance role that is played by a reference genome when used during sequence alignment. Stephen A. Fisher, Junhyong Kim, Dan Berrios reference genome role reference genome-transcriptome alignment algorithm An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome. Stephen A. Fisher, Junhyong Kim, Dan Berrios reference genome-transcriptome alignment algorithm sequence read length measurement datum A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence. Stephen A. Fisher, Junhyong Kim, Dan Berrios read length, read length measurement datum sequence read length measurement datum sequencing library input quantity measurement datum A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer. Stephen A. Fisher, Junhyong Kim library input amount sequencing library input quantity measurement datum single-end library A cDNA library that is a collection of short tags from only one end of DNA fragments. Stephen A. Fisher, Junhyong Kim, Dan Berrios single-end library specimen harvest quantity A scalar measurement datum that indicates the amount of specimen collected. Stephen A. Fisher, Junhyong Kim, Dan Berrios harvest quantity specimen harvest quantity spike-in dilution factor A data item that indicates the dilution of spike-in added to a specimen. Stephen A. Fisher, Junhyong Kim, Dan Berrios spike-in dilution factor star algorithm A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference. Stephen A. Fisher, Junhyong Kim, Dan Berrios https://www.ncbi.nlm.nih.gov/pubmed/23104886 star algorithm A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions. Dan Berrios Junhyong Kim Stephen A. Fisher transcript analysis by single-end sequencing url:https://www.illumina.com/science/technology/next-generation-sequencing/paired-end-vs-single-read-sequencing.html transcript analysis by single-end sequencing assay verse algorithm An alignment counting algorithm that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads. Stephen A. Fisher, Junhyong Kim http://kim.bio.upenn.edu/software/verse.shtml or http://biorxiv.org/content/early/2016/05/14/053306 verse algorithm microraft A material separation device also commerically known as Isoraft, that is used to isolate single cells. Stephen A. Fisher, Junhyong Kim, Dan Berrios https://en.wikipedia.org/wiki/Microrafts microraft pipette A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser. Stephen A. Fisher, Junhyong Kim, Dan Berrios https://en.wikipedia.org/wiki/Pipette pipette An organism detection assay that uses a differential medium to achieve its objective. John Judkins EuPathDB, https://www.uwyo.edu/molb2210_lab/info/biochemical_tests.htm differential medium assay A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material John Judkins medication timepoint OBI VEuPathDB medication time value specification A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment John Judkins medication dose OBI VEuPathDB medication dose value specification A role that is borne by a case-control study design participant under investigation that is associated with the outcome mentioned in the study design. John Judkins, Bjoern Peters OBI case role in case-control study A role that is borne by a case-control study design participant under investigation that is not associated with the outcome mentioned in the study design. John Judkins, Bjoern Peters OBI control role in case-control study A specimen that is derived from amniotic fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank amniotic fluid specimen A specimen that is derived from bile. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank bile specimen A specimen that is derived from cerbrospinal fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank cerebrospinal fluid specimen A specimen that is derived from feces. Chris Stoeckert stool specimen Chris Stoeckert, Penn Medicine Biobank feces specimen A specimen that is derived from digestive system fluid or secretion. Chris Stoeckert gastric fluid specimen Chris Stoeckert, Penn Medicine Biobank digestive system fluid or secretion specimen A specimen that is derived from milk. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank milk specimen A specimen that is derived from pericardial fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank pericardial fluid specimen A specimen that is derived from saliva. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank saliva specimen A specimen that is derived from sputum. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank sputum specimen A specimen that is derived from sweat. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank sweat specimen A specimen that is derived from synovial fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank synovial fluid specimen A specimen that is derived from vireous humor. Chris Stoeckert vitreous fluid specimen Chris Stoeckert, Penn Medicine Biobank vitreous humor specimen A specimen that is derived from bone marrow. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank bone marrow specimen A specimen that is derived from placenta. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank placenta specimen A specimen that is derived from peritoneal fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank peritoneal fluid specimen A specimen that is derived from pleural fluid. Chris Stoeckert Chris Stoeckert, Penn Medicine Biobank pleural fluid specimen A specimen that is derived from brain. Chris Stoeckert Chris Stoeckert, NCI BBRB brain specimen A specimen that is derived from hair. Chris Stoeckert Chris Stoeckert, NCI BBRB hair specimen A specimen that is derived from prostate gland. Chris Stoeckert Chris Stoeckert, NCI BBRB prostate gland specimen A specimen that is derived from skeletal muscle. Chris Stoeckert Chris Stoeckert, NCI BBRB skeletal muscle tissue specimen A specimen that is derived from heart. Chris Stoeckert Chris Stoeckert, NCI BBRB heart specimen A specimen that is derived from renal medulla. Chris Stoeckert kidney medulla specimen Chris Stoeckert, NCI BBRB renal medulla specimen A specimen that is derived from adrenal gland. Chris Stoeckert Chris Stoeckert, NCI BBRB adrenal gland specimen A specimen that is derived from breast. Chris Stoeckert mammary tissue specimen Chris Stoeckert, NCI BBRB breast specimen A specimen that is derived from urinary bladder. Chris Stoeckert Chris Stoeckert, NCI BBRB urinary bladder specimen A specimen that is derived from tibial artery. Chris Stoeckert Chris Stoeckert, NCI BBRB tibial artery specimen A specimen that is derived from skin. Chris Stoeckert skin specimen Chris Stoeckert, NCI BBRB skin of body specimen A specimen that is derived from pancreas. Chris Stoeckert Chris Stoeckert, NCI BBRB pancreas specimen A specimen that is derived from stomach. Chris Stoeckert Chris Stoeckert, NCI BBRB stomach specimen A specimen that is derived from pituitary gland. Chris Stoeckert Chris Stoeckert, NCI BBRB pituitary gland specimen A specimen that is derived from adipose tissue. Chris Stoeckert Chris Stoeckert, NCI BBRB adipose tissue specimen A specimen that is derived from cortex of kidney. Chris Stoeckert kidney cortex specimen Chris Stoeckert, NCI BBRB cortex of kidney specimen A specimen that is derived from esophagus mucosa. Chris Stoeckert Chris Stoeckert, NCI BBRB esophagus mucosa specimen A specimen that is derived from colon. Chris Stoeckert Chris Stoeckert, NCI BBRB colon specimen A specimen that is derived from lung. Chris Stoeckert Chris Stoeckert, NCI BBRB lung specimen A specimen that is derived from esophagus muscularis mucosa. Chris Stoeckert esophagus muscularis specimen Chris Stoeckert, NCI BBRB esophagus muscularis mucosa specimen A specimen that is derived from cerebral cortex. Chris Stoeckert brain cortex specimen Chris Stoeckert, NCI BBRB cerebral cortex specimen A specimen that is derived from thyroid gland. Chris Stoeckert Chris Stoeckert, NCI BBRB thyroid gland specimen A specimen that is derived from cerebellum. Chris Stoeckert brain cerebellum specimen Chris Stoeckert, NCI BBRB cerebellum specimen A specimen that is derived from tibial nerve. Chris Stoeckert Chris Stoeckert, NCI BBRB tibial nerve specimen A specimen that is derived from coronary artery. Chris Stoeckert Chris Stoeckert, NCI BBRB coronary artery specimen A specimen that is derived from spleen. Chris Stoeckert Chris Stoeckert, NCI BBRB spleen specimen A specimen that is derived from aorta. Chris Stoeckert Chris Stoeckert, NCI BBRB aorta specimen A specimen that is derived from the atrium auricular region. Chris Stoeckert Chris Stoeckert, NCI BBRB atrial appendage specimen A specimen that is derived from the esophagogastric junction. Chris Stoeckert Chris Stoeckert, NCI BBRB esophagogastric junction specimen A specimen that is derived from ileum. Chris Stoeckert Chris Stoeckert, NCI BBRB ileum specimen A specimen that is derived from liver. Chris Stoeckert Chris Stoeckert, NCI BBRB liver specimen A specimen that is derived from minor salivary gland. Chris Stoeckert Chris Stoeckert, NCI BBRB minor salivary gland specimen A specimen that is derived from omentum. Chris Stoeckert Chris Stoeckert, NCI BBRB omentum specimen A specimen that is derived from female gonad. Chris Stoeckert Chris Stoeckert, NCI BBRB ovary specimen A specimen that is derived from sigmoid colon. Chris Stoeckert Chris Stoeckert, NCI BBRB sigmoid colon specimen A specimen that is derived from suprapubic skin. Chris Stoeckert Chris Stoeckert, NCI BBRB suprapubic skin specimen A specimen that is derived from testis. Chris Stoeckert Chris Stoeckert, NCI BBRB testis specimen A specimen that is derived from uterus. Chris Stoeckert Chris Stoeckert, NCI BBRB uterus specimen A specimen that is derived from vagina. Chris Stoeckert Chris Stoeckert, NCI BBRB vagina specimen "18-33 years old" An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen https://github.com/obi-ontology/obi/issues/839 age group inclusion criterion A value specifcation that specifies the youngest age when specifying an age range. Mathias Brochhausen minimum age value specification A value specifcation that specifies the oldest age when specifying an age range. Mathias Brochhausen maximum age value specification "received at least 2 days of vancomycin" An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process. Mathias Brochhausen https://github.com/obi-ontology/obi/issues/840 use of medication inclusion criterion "included hospital patients" An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process. Mathias Brochhausen hospital patient inclusion criterion "included married and unmarried patients", "included divorced individuals" An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process. Mathias Brochhausen family status inclusion criterion "included males and females", "included male patients" An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen sex inclusion criterion "include US residents" An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process. Mathias Brochhausen country of residence inclusion criteria "include only Hispanic individuals" An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process. Mathias Brochhausen ethnicity inclusion criterion A histological assay that is intended to check for the presence or level of a specific disease. OBI histopathology assay A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed). Dan Berrios Dan Berrios adapter-sequence trimming A data transformation in which data contained in 2 or more files are merged into a single file. Dan Berrios Dan Berrios file merge A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm. Dan Berrios Dan Berrios sequence alignment The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables. Dan Berrios Dan Berrios sequence data feature count tabulation The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed, to achieve some specific objective. Dan Berrios Dan Berrios trimmed sequence data Kolbert, Christopher P., et al. "Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues." PloS one 8.1 (2013): e52517. PMID:23382819 A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays. PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg. Mark A. Miller added based on http://purl.obolibrary.org/obo/OBI_0002013 https://www.nanostring.com/products/mirna-assays/mirna-panels nCounter Mouse miRNA Expression array A transcription profiling by RNA sequencing assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing. Jason Hilton Mark A. Miller Michelle Giglio Sebastian Duesing mRNA-seq url:https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-419 ENCODE polyA-selected RNA sequencing assay A transcription profiling by RNA sequencing assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing. Jason Hilton Mark A. Miller Michelle Giglio Sebastian Duesing polyA-depleted RNA-seq url:http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030733 url:http://www.tandfonline.com/doi/full/10.1080/15476286.2015.1110676 ENCODE polyA-depleted RNA sequencing assay A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified. Mark A. Miller, based on http://purl.obolibrary.org/obo/OBI_0000869 PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group polyA depleted RNA extract RNA extraction with polyA depletion A RNA extraction process in which only RNAs lacking a polyA tail are retained Mark A. Miller, based on OBI_0000848 UPenn Group 2018-05-11T15:01:14Z RNA extraction with polyA depletion Novel transcript forms were assessed by isoform sequencing. A transcription profiling by RNA sequencing assay for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms. Michelle Giglio Sebastian Duesing ISO-seq url:http://www.pacb.com/blog/intro-to-iso-seq-method-full-leng/ isoform sequencing Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run. Dan Berrios Dan Berrios adapter sequence data The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed. Dan Berrios Dan Berrios adapter-trimmed sequence data The results of a sequence alignment. Dan Berrios Dan Berrios aligned sequence data The results of a data transformation of sequence data in which files containing aligned sequence data are merged together Dan Berrios Dan Berrios merged aligned sequence data The results of a sequence data feature count tabulation. Dan Berrios Dan Berrios sequence library feature count data The results of a DNA methylation profiling assay DNA methylation profiling data The results of a differential expression analysis. differential expression analysis data A data transformation in which subsequences of a molecular sequence are cut (removed). sequence trimming digital acquisition card The digital acquisition card acts as the interface between the computer and a measurement device via the computer bus. It converts the signal generated by a measurement device (output from device) to a digital signal via an analog-to-digital converter, ADC. It also converts a digital signal to an analog signal via a digital-to-analog converter, DAC. This analog signal (e.g., stimulus) is fed to a measurement device (input to device). Mark A. Miller DAQ device digital acquisition and digital generation card Brenda Farrell, bfarrell@bcm.edu digital acquisition card machine learning A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability. Mark A. Miller https://en.wikipedia.org/wiki/Machine_learning https://github.com/TrisSN machine learning supervised machine learning A machine learning process using a function that maps an input to an output based on example input-output pairs. It infers a function from labeled training data consisting of a set of training examples. Mark A. Miller https://en.wikipedia.org/wiki/Supervised_learning https://github.com/TrisSN supervised machine learning unsupervised machine learning A machine learning process that infers a function describing the structure of "unlabeled" data (i.e. data that has not been classified or categorized). Mark A. Miller https://en.wikipedia.org/wiki/Unsupervised_learning https://github.com/TrisSN unsupervised machine learning A study design that investigates the features of interaction between molecules. Rebecca Jackson person:RCT molecular interaction identification design A molecular interaction identification design that investigates the co-occurence and correlation of two or more molecules. Rebecca Jackson url:https://en.wikipedia.org/wiki/Colocalization colocalization identification design A molecular interaction identification design that investigates a phenotype that is the result of two or more genetic perturbations, and is not explained by the individual genetic perturbations alone. Rebecca Jackson MI:0208 genetic interaction identification design A molecular interaction identification design that investigates a relationship that is the result of intermediate steps between two or more molecules that are not necessarily in direct contact with each other. Rebecca Jackson MI:2286 functional association identification design A molecular interaction identification design that investigates the influence of molecules, which are in direct contact, on one another. Rebecca Jackson molecular binding identification design MI:0407 direct interaction identification design A direct interaction identification design that investigations a biological reaction on a molecule which has been triggered by an enzyme. Rebecca Jackson MI:0414 enzymatic reaction identification design A molecular interaction identification design that investigates intra-molecular interactions between two or more regions of a single molecule. Rebecca Jackson MI:1126 self interaction identification design A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing. Rebecca Jackson 3C-seq assay PMID:23411633 https://github.com/obi-ontology/obi/issues/939 chromosome conformation capture sequencing assay A polymerase chain reaction which amplifies DNA with only one known sequence from which primers may be designed. A series of restriction digestions and ligations result in a looped DNA fragment which can be primed for PCR. Rebecca Tauber inverse PCR url:https://en.wikipedia.org/wiki/Chromosome_conformation_capture inverse polymerase chain reaction swab specimen A specimen that is stored on a swab as the output of a collecting specimen with swab process. Chris Stoeckert OBIB/OBI https://github.com/obi-ontology/obi/issues/910 OBIB swab specimen collecting specimen with swab A specimen collection process that uses a swab as the collection device. A swab is an absorbent material (e.g. cotton) on a rod (e.g., wooden stick). Chris Stoeckert OBIB https://github.com/obi-ontology/obi/issues/910 OBIB collecting specimen with swab Sequence data in which an identifier subsequence has been used to categorize each reads by source. Dan Berrios Dan Berrios demultiplexed sequence data Sequence data from a sequence library generated from at least two different sources, where each read in the sequence data includes base calls from a multiplex identifier sequence that can be used to trace the source of the read to its source. Dan Berrios Dan Berrios multiplexed sequence data A specimen that is collected with a swab from the surface of an areola of a breast. Chris Stoeckert Chris Stoeckert, OBIB areolar swab specimen A specimen that is collected with a swab from the surface of a breast. Chris Stoeckert Chris Stoeckert, OBIB breast swab specimen A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth. Chris Stoeckert Chris Stoeckert, OBIB cheek swab specimen A specimen that is collected with a swab from the surface of a nasopharynx. Chris Stoeckert Chris Stoeckert, OBIB nasopharyngeal swab specimen A specimen that is collected with a swab from the inside surface of a mouth. Chris Stoeckert Chris Stoeckert, OBIB oral swab specimen A specimen that is collected with a swab from the surface of a oropharynx. Chris Stoeckert Chris Stoeckert, OBIB oropharyngeal swab specimen A specimen that is collected with a swab from the surface of a rectum. Chris Stoeckert Chris Stoeckert, OBIB rectal swab specimen A specimen that is collected with a swab from the surface of a tongue. Chris Stoeckert Chris Stoeckert, OBIB tongue swab specimen A specimen that is collected with a swab from the surface of a vagina. Chris Stoeckert Chris Stoeckert, OBIB vagina swab specimen A specimen that is collected with a swab from the surface of a feces. Chris Stoeckert stool swab specimen Chris Stoeckert, OBIB fecal swab specimen A specimen that is collected with a swab from the surface of an environmenal material. Chris Stoeckert Chris Stoeckert, OBIB environmental swab specimen The LucKi Birth Cohort Study was designed and started in 2006 to follow children from birth into adulthood on a wide range of determinants, disorders, and diseases. A cohort study design for which the subjects are followed from the time of birth usually including information about gestation and follow up. MIABIS MIABIS contributors birth cohort study design A study of the symptoms experienced by patients who have been diagnosed with multiple sclerosis employs a disease specific study design. A study design for which material and information is collected from subjects that have already developed a particular disease. MIABIS MIABIS contributors disease specific study design A family tree is a type of genealogical record. A document about the family relationships of persons related as members of a domestic group linked through descent from a common ancestor, marriage, or adoption. MIABIS Sarah Bost genealogical record The Social Security Administration's Death Master File is a national registry in the United States. An information content entity that contains information about a nationwide group of individuals. MIABIS Sarah Bost MIABIS contributors national registry The Care Register for Health Care, maintained by the Finnish National Institute for Health and Welfare, is a national biomedical registry. A national registry that contains information about individuals that was accumulated for a biomedical purpose, such as diagnoses, treatments, or outcomes. MIABIS Sarah Bost MIABIS contributors national biomedical registry Site-directed mutagenesis was used to prepare mutants of the Hypoxia-inducible factor-1 (HIF-1) alpha subunit to investigate the role of certain amino acids in hypoxia. (PMID:12393189) An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer. Rebecca Jackson url:https://www.ncbi.nlm.nih.gov/books/NBK21945/ https://github.com/obi-ontology/obi/issues/1058 site-directed mutagenesis Error-prone PCR was used to introduce amino acid mutations to the cAMP receptor protein (CRP) of E. coli to investigate strain engineering to improve osmotolerance for industrial requirements. (PMID:22179860) An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR. Rebecca Jackson PMID:15153637 https://github.com/obi-ontology/obi/issues/1058 random mutagenesis "In an attempt to define the mechanism of insulin-regulated glucose transporter 4 (Glut4) translocation, we have developed an in vitro reconstitution assay... insulin-induced Glut4 translocation can be reconstituted in vitro to a limited extent by using isolated membranes." (PMID:10611313) An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together. Rebecca Jackson reconstitution experiment url:https://jcs.biologists.org/content/132/4/jcs227488 https://github.com/obi-ontology/obi/issues/1059 reconstitution assay An in vitro reconstituted mouse transcription system helped identify an NF-Y interacting promoter as essential for high-level expression from the R2 promoter. (PMID:11502214) A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components. Rebecca Jackson PMID:9237163 https://github.com/obi-ontology/obi/issues/1059 in vitro transcription reconstitution assay A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample. Whole metagenome sequencing has been used to explore the composition and metabolic capability of communities of microbes found in the environment (e.g. in soil, water, etc.) and in humans and other species (e.g. in the gut, oral cavity, etc.). Rebecca Jackson WMS Bjoern Peters Michelle Giglio https://github.com/obi-ontology/obi/issues/1056 whole metagenome sequencing assay A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants. John Judkins, Bjoern Peters Wikipedia, OBI case-control study design A genetic transformation which reduces the expression of a specific gene or genes in an organism. Rebecca Jackson gene knock-down url:https://en.wikipedia.org/wiki/Gene_knockdown gene knockdown A gene knockdown that silences genes through artificially-induced RNA interference. This is accomplished by introducing small double-stranded interfering RNA complementary to the target mRNA to be silenced, which is then cleaved by a ribonuclease. Rebecca Jackson RNA interference gene knockdown url:https://en.wikipedia.org/wiki/Gene_knockdown RNAi gene knockdown ribosomal RNA-depleted RNA extract Looking at the reads for each ribosomal RNA-depleted RNA extract, the vast majority align to protein coding genes based on the ENSEMBL annotation. An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species). Dan Berrios https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4585-1 ribosomal RNA-depleted RNA extract "Here, we described the development of RNAi by micro-injection of double-stranded RNA (dsRNA) in the pea aphid Acyrthosiphon pisum. Injection of dsRNA into whole aphid body induced the silencing of two marker genes with different expression patterns: the ubiquitously expressed Ap-crt genes encoding a calreticulin and the gut specific Ap-cath-L gene encoding a cathepsin-L." (PMID:17903251) A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts. Rebecca Jackson RNA interference knockdown assay RNAi gene knockdown assay Rebecca Jackson https://github.com/obi-ontology/obi/issues/1057 RNAi knockdown assay An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA. Dan Berrios DRS direct RNA-seq url:https://www.nature.com/articles/nature08390 https://github.com/obi-ontology/obi/issues/874 jahilton direct RNA sequencing assay Illumina NovaSeq 6000 Genomic DNA of Xenophilus sp. E41 was extracted and sequenced using an Illumina NovaSeq 6000 system. A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. Dan Berrios NovaSeq 6000 http://www.illumina.com/systems/sequencing-platforms/novaseq.html Illumina NovaSeq 6000 Single-cell RNA sequencing (scRNA-seq) assays provide the expression profiles of individual cells. A transcription profiling by RNA sequencing assay that uses as input RNA extracts that can be traced to a single cell of origin. These extracts may come from the entire cell or only a part of the cell such as the nucleus or the cytoplasm. Dan Berrios Michelle Giglio Sebastian Duesing scRNA-seq single-cell RNA sequencing assay single-cell RNA-seq Anna Maria Masci Michelle Giglio single-cell transcription profiling by RNA sequencing assay PacBio Sequel The cDNAs were sequenced on the PacBio Sequel platform. A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation Bonita Lam Dan Berrios Pacific BioSciences Sequel http://www.pacb.com/products-and-services/pacbio-systems/sequel/ PacBio Sequel PacBio Sequel II The cDNAs were sequenced on the PacBio Sequel II platform. A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ("HiFi") long reads, and which is manufactured by the Pacific Biosciences corporation. Bonita Lam Dan Berrios Pacific BioSciences Sequel II http://www.pacb.com/products-and-services/pacbio-systems/sequel/ PacBio Sequel II An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB disease exacerbation after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific antibodies or B cells An efficacy of T cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specfic T cells. IEDB IEDB decreased disease after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells An efficacy of B cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB decreased disease after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific disease reduction resulting from adoptive transfer of epitope specific antibodies or B cells An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specfic T cells. IEDB IEDB protection from challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB protection from challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. IEDB IEDB pathogen burden after challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden. IEDB IEDB pathogen burden after challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden An in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells using survival. IEDB IEDB survival from other challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells based on survival An in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. IEDB IEDB survival from other challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using tumor burden. IEDB IEDB tumor burden after challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on tumor burden An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using tumor burden. IEDB IEDB tumor burden after challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on tumor burden An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specfic T cells. IEDB IEDB tolerance after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB tolerance after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells Cytogenetics; the histopathological diagnosis of malaria and other parasites; differentiate nuclear and cytoplasmic morphology of the various blood cells like platelets, RBCs, WBCs An assay that uses a Giemsa stain to characterize cells. Chris Stoeckert Jie Zheng https://github.com/obi-ontology/obi/issues/1093 VEuPathDB Giemsa stain assay 1 A specimen composed of an individual organism to be studied in an investigation. Person: Jie Zheng EFO_0000542 individual https://github.com/obi-ontology/obi/issues/1092 individual organism specimen An organism detection assay that detects microorganisms in a blood specimen. John Judkins https://github.com/obi-ontology/obi/issues/1064 blood microbiology assay Biopsy of a potentially cancerous mole. A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive. Damion Dooley Nicole Vasilevsky https://en.wikipedia.org/wiki/Biopsy biopsy Image-guided needle biopsy allows a doctor to biopsy suspicious areas that aren't readily seen or felt through skin, such as in a prostate gland. A biopsy which uses an imaging procedure to guide a needle biopsy. Damion Dooley image guided needle biopsy image-guided biopsy imaging guided biopsy https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 image guided biopsy A CT Guided Biopsy is a procedure performed by a radiologist to obtain a small tissue sample through a needle. A needle biopsy guided by real-time computed tomography (CT) scan images. Damion Dooley CT Assisted Biopsy CT Guided Biopsy Computed Tomography Assisted Biopsy Computed Tomography-Guided Needle Biopsy http://purl.obolibrary.org/obo/NCIT_C137909 computed tomography assisted biopsy An ultrasound-guided needle biopsy uses sound waves to help locate a nodule or abnormality within the thyroid. A needle biopsy guided by ultrasound visualization. Damion Dooley https://www.oncolink.org/cancer-treatment/procedures-diagnostic-tests/biopsy-procedures/ultrasound-guided-needle-biopsy ultrasound-guided needle biopsy A needle biopsy is often used on suspicious breast lumps and enlarged lymph nodes that a doctor can feel through a patient's skin. A biopsy that uses a hollow needle to extract cells. Damion Dooley https://www.mayoclinic.org/tests-procedures/needle-biopsy/about/pac-20394749 needle biopsy A fine needle aspiration biopsy is commonly performed in order to test for cancer. A biopsy that uses a thin needle to extract cells. Chris Stoeckert, Helena Ellis, Jie Zheng FNA FNAB https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ NCI BBRB fine needle aspiration biopsy A core needle biopsy can remove more tissue than a fine needle biopsy, and therefore can provide more information about the cells and tissue removed. A biopsy that uses a hollow tube to collect a core of tissue. Chris Stoeckert, Helena Ellis, Jie Zheng CNB https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ NCI BBRB core needle biopsy Surgical biopsy may be required to collect hard-to-reach tissue. A biopsy involving a surgical incision into an organism to access the biopsy material. Damion Dooley excisional biopsy open biopsy https://www.mayoclinic.org/diseases-conditions/cancer/in-depth/biopsy/art-20043922 surgical biopsy The makeup of fat in the abdominal wall can be investigated by fat biopsy. A biopsy involving the collection of a small part of the abdominal wall fat pad. Nicole Vasilevsky, Damion Dooley abdominal wall biopsy fat biopsy https://www.ucsfbenioffchildrens.org/tests/003841.html abdominal wall fat pad biopsy A mouse tail biopsy was performed to collect material for DNA extraction. A biopsy involving the collection of the tip of a mamallian tail. Nicole Vasilevsky, Damion Dooley snip http://web.jhu.edu/animalcare/policies/Tail%20Biopsy%20of%20Mice.pdf tail biopsy A bone marrow biopsy removes bone with the marrow inside to look at under a microscope A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected. Nicole Vasilevsky http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy bone marrow biopsy A three or four millimeter punch is used in s skinpunch biopsy proceedure. A biopsy that involves the collection of a cylinder of skin (including epidermis, dermis and superficial fat) using a punch tool. Nicole Vasilevsky punch biopsy; skin biopsy http://healthlibrary.epnet.com/GetContent.aspx?token=b93d114e-5009-4f6a-9917-6c594254fcc7&chunkiid=14861 skinpunch biopsy A cytometric bead array assay that detects interleukin-15 production by T cells. IEDB IEDB IL-15 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-15 production by T cells A cytometric bead array assay that detects interleukin-16 production by T cells. IEDB IEDB IL-16 release|cytometric bead array cytometric bead array assay measuring epitope specific interleukin-16 production by T cells An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB hypersensitivity after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope specfic T cells. IEDB IEDB type IV hypersensitivity (DTH) after adoptive transfer|in vivo skin test in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells A T cell epitope specific proliferation assay that is performed in vivo after adoptive transfer of epitope specfic T cells. IEDB IEDB proliferation after adoptive transfer|in vivo assay in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive transfer of epitope specfic T cells. IEDB IEDB antibody help after adoptive transfer|in vivo assay assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive transfer of epitope specfic T cells. IEDB IEDB T cell help after adoptive transfer|in vivo assay assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells An in vivo cell killing assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC after adoptive transfer of epitope specific T cells. IEDB IEDB cytotoxicity after adoptive transfer|in vivo assay in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells An enzyme-linked immunosorbent assay that detects epitope specific perforin release by T cells. IEDB IEDB perforin release|ELISA ELISA measuring epitope specific perforin release by T cells Selenite broth is an enrichment culture medium used to selectively isolate Salmonella species. A culture medium that is designed to favor the growth of a particular microorganism or cells over others, enriching a sample for the microorganism or cells of interest. isolation medium 2020-03-08T22:04:07Z enrichment culture medium case series study design PMID: 22213493 A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included. http://orcid.org/0000-0002-8844-9165 https://www.ncbi.nlm.nih.gov/pubmed/22213493 case series design An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences. Damion Dooley MPRA https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364389/ massively parallel reporter assay An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic T cells. IEDB IEDB in vivo response after adoptive transfer|in vivo assay in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB in vivo response after adoptive transfer|in vivo assay in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specfic T cells. IEDB IEDB disease exacerbation after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells vacuum-assisted biopsy needle Vacuum-assisted biopsy needles come in two varieties: a non-tethered design and a needle design requiring tethering cable to a vacuum source. A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material. Damion Dooley https://www.researchgate.net/publication/330227873 https://github.com/obi-ontology/obi/issues/1163 vacuum-assisted biopsy needle “Inhibition of MERS-CoV-spike-mediated pseudovirus entry by the HKU4 S1 domain “ (from https://doi.org/10.1073/pnas.1405889111); “protease treatment did not enhance pseudotype entry in the absence of host receptor “; “bat-derived cell lines derived from other species were infected with VSV-reporter particles pseudotyped with chimeric spikes and luciferase was measured as readout for cell entry” (from https://doi.org/10.1038/s41564-020-0688-y) ; “teicoplanin could inhibit the entry of HIV-1-2019-nCoV-S pseudoviruses with the IC50 value of 1.66 uM” (from https://doi.org/10.1101/2020.02.05.935387) An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest. Thomas Lemberger pseudotype cell entry pseudotype entry pseudotyped particle cell entry assay pseudovirus cell entry Figure 1c in https://doi.org/10.1038/s41564-020-0688-y or Materials & Method in https://www.pnas.org/content/111/34/12516 pseudovirus entry assay glass bottle A container with a narrow neck that is made of glass. VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB glass bottle glass bottle coated with insecticides A glass bottle that coated with material designed to control insects. VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB glass bottle coated with insecticides A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs). Jie Zheng short interspersed elements PCR PMID: 12711348 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB short interspersed nuclear elements polymerase chain reaction A polymerase chain reaction with modification intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. The nested polymerase chain reaction (PCR) involves the use of two primer sets and two successive PCR reactions. The first set of primers are designed to anneal to sequences upstream from the second set of primers and are used in an initial PCR reaction. Jie Zheng nested PCR nested-PCR https://en.wikipedia.org/wiki/Nested_polymerase_chain_reaction https://github.com/obi-ontology/obi/issues/1117 VEuPathDB nested polymerase chain reaction An electrophoresis that separates and characterize proteins based on reaction with antibodies. Jie Zheng IEP https://en.wikipedia.org/wiki/Immunoelectrophoresis https://github.com/obi-ontology/obi/issues/1117 VEuPathDB immunoelectrophoresis An electrophoresis in which antigen and antibody move in opposite directions and form precipitates in the area between the cells where they meet in concentrations of optimal proportions. Jie Zheng http://www.ispybio.com/search/protocols/ie%20protocol2.pdf https://github.com/obi-ontology/obi/issues/1117 VEuPathDB counter current immunoelectrophoresis A linear amplification that uses a thermostable ligase to amplify a piece of DNA. Because the enzyme retains activity after multiple thermal cycles, the ligations may be repeated to linearly increase product. Jie Zheng LDR MIRO:20000103 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB ligase detection reaction An enzymatic amplification in which a piece of DNA is amplified at a constant temperature of 60 - 65 degree C using either two or three sets of primers and a polymerase with high strand displacement activity in addition to a replication activity. This amplification does not need thermal cyclers and may be a low cost alternative to PCR. Jie Zheng LAMP https://en.wikipedia.org/wiki/Loop-mediated_isothermal_amplification https://github.com/obi-ontology/obi/issues/1117 VEuPathDB loop-mediated isothermal amplification An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms. Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB detection of pathogenic organisms objective An organism feature identification objective that aims to detect insecticide resistance of an insect. Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance detection objective A specimen used in a blood meal assay to determine what is the source of blood ingested by a mosquito. A specimen of the blood ingested by an arthropod. The mosquito feeds on a human for example, ingests the blood of the human, this blood is then taken from the tummy of a mosquito and a PCR may be run on this specimen to identify that the mosquito definitely fed on a human. Chris Stoeckert Jie Zheng blood meal VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB arthropod meal of blood specimen An assay that uses polymerase chain reaction technique to amplify DNA. VEuPathDB VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB polymerase chain reaction assay An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences. VEuPathDB RFLP restriction fragment length polymorphism restriction fragment length polymorphism analysis https://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism https://github.com/obi-ontology/obi/issues/1117 VEuPathDB restriction fragment length polymorphism assay An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA. VEuPathDB DNA finger printing DNA fingerprint DNA fingerprinting DNA profiling VEuPathDB https://github.com/obi-ontology/obi/issues/1117 VEuPathDB DNA fingerprinting assay An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population. VEuPathDB resistance identification/monitoring MIRO:20000001 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance assay An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes. VEuPathDB monitoring known mutations MIRO:20000096 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by monitoring known mutations assay An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes. VEuPathDB metabolic resistance assay MIRO:20000003 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting enzyme activity assay An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism. VEuPathDB bioassay MIRO:20000058 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance bioassay An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase. VEuPathDB alpha esterase activity assay IRO:0000149 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting alpha esterase activity assay An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase. VEuPathDB beta esterase activity assay IRO:0000150 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting beta esterase activity assay An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase. VEuPathDB AChE activity assay AChE assay acetylcholinesterase assay MIRO:20000010 MIRO:20000084 MIRO:20000086 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting acetylcholinesterase activity assay An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST). VEuPathDB GST related assay MIRO:20000083 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting glutathione S-transferase activity assay An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate. VEuPathDB pNPA assay MIRO:20000019 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting carboxylic ester hydrolase activity assay An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present. VEuPathDB mixed-function oxidase assay MIRO:20000062 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by detecting mixed-function oxidase assay An insecticide resistance bioassay without the use of any synergist. VEuPathDB direct bioassay MIRO:20000044 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB direct insecticide resistance bioassay An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect. VEuPathDB topical application assay IRO:0000155 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB topical application insecticide resistance bioassay A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population. VEuPathDB diagnostic test MIRO:20000075 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB direct insecticide resistance diagnostic assay A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance. VEuPathDB dose response test MIRO:20000076 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance dose response assay A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide. VEuPathDB time response test MIRO:20000013 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance time response assay A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations. VEuPathDB CDC bottle bioassay MIRO:20000009 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB Centre for Disease Control and Prevention bottle bioassay A direct insecticide resistance diagnostic assay uses WHO cone kit. VEuPathDB cone DT MIRO:20000039 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB WHO cone kit diagnostic assay A direct insecticide resistance diagnostic assay uses WHO paper kit. VEuPathDB WHO paper kit DT MIRO:20000041 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB WHO paper kit diagnostic assay A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide. VEuPathDB WHO larvicide DT MIRO:20000049 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB WHO larvicide diagnostic assay An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides. VEuPathDB bottle bioassay DR test MIRO:20000011 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance dose response by bottle assay An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide. VEuPathDB WHO larvicide DR test MIRO:20000050 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance dose response by survival of larvae assay An insecticide resistance dose response assay using WHO paper kit. VEuPathDB WHO paper kit DR test MIRO:20000048 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance dose response by WHO paper kit assay An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist. VEuPathDB bottle bioassay TR test MIRO:20000030 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance time response by bottle assay An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist. VEuPathDB WHO paper kit TR test MIRO:20000036 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance time response by WHO paper kit assay An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations. VEuPathDB ARMS Amplification Refractory Mutation System IRO:0000006 PMID: 18428319 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by amplification refractory mutation system assay An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes. VEuPathDB PIRA-PCR Primer Introduced Restriction Analysis PCR polymerase chain reaction-primer-introduced restriction analysis IRO:0000007 PMID: 8339229 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by primer introduced restriction analysis PCR assay An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique. VEuPathDB gene mutation detection by nested PCR IRO:0000127 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by nested polymerase chain reaction assay An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix. VEuPathDB MIRO:20000103 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by ligase detection reaction assay An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction. VEuPathDB gene mutation detection by LDR-FMA ligase detection reaction-fluorescent microsphere assay IRO:0000151 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by ligase detection reaction-fluorescent microsphere assay An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles. VEuPathDB PASA PCR amplification of specific alleles allele-specific amplification and amplification refractory mutation system PMID: 1734929 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by PCR amplification of specific alleles assay An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation. VEuPathDB MIRO:20000102 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by fluorogenic PCR assay An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay. VEuPathDB PCR-RFLP MIRO:20000113 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by PCR-RFLP assay An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs). VEuPathDB Short Interspersed Elements PCR IRO:0000013 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB insecticide resistance by short interspersed elements PCR assay An organism detection assay that detects pathogens. VEuPathDB pathogen detection method IRO:0000137 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB pathogen detection assay A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip. VEuPathDB VectorTest IRO:0000138 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB VectorTest assay A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances. VEuPathDB Rapid Analyte Measurement Platform IRO:0000164 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB pathogen detection by Rapid Analyte Measurement Platform assay A pathogen detection assay that is based on loop-mediated isothermal amplification. VEuPathDB Loop-mediated isothermal amplification IRO:0000165 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB pathogen detection by loop-mediated isothermal amplification assay An assay that analyzes the specimen taken from blood meal fed organism, such as insect. VEuPathDB blood meal analysis IRO:0000135 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB blood meal assay A blood meal assay that uses a counter current immunoelectrophoresis technique. VEuPathDB CIE countercurrent immunoelectrophoresis IRO:0000136 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB blood meal by counter current immunoelectrophoresis assay A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect. VEuPathDB DNA based blood meal finger printing VEuPathDB VSMO:0001307 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB DNA based blood meal finger printing assay An organism detection assay that is based on the size of organism. VEuPathDB by size IRO:0000145 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by size assay An organism detection assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced. VEuPathDB cross mating experiment MIRO:30000036 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by cross mating assay An organism detection assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species. VEuPathDB cytological chromosome examination MIRO:30000037 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by cytological chromosome examination assay An organism detection assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species. VEuPathDB isoenzyme electrophoresis MIRO:30000038 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by isoenzyme electrophoresis assay An organism detection assay that is based on examination of morphology and the use of specific taxonomic keys to determine the species of the specimen. VEuPathDB morphological examination MIRO:30000039 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by morphological examination assay An organism detection assay that is based on PCR. VEuPathDB PCR-based species identification MIRO:30000040 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by PCR assay An organism detection assay that is based on DNA hybrdization. VEuPathDB species specific DNA hybridization MIRO:30000041 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by specific DNA hybridization assay An organism detection assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species. VEuPathDB salinity tolerance tests MIRO:30000042 https://github.com/obi-ontology/obi/issues/1117 VEuPathDB organism detection by salinity tolerance assay molecular label role A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay. MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role). JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced REO_0000171 by newly assigned ID: OBI:0002743. Group: OBI molecular tracer role OBI developer call, 3-12-12 https://github.com/obi-ontology/obi/issues/1135 molecular label role molecular label A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay JZ (3-30-20): discussed on the OBI call. Since the REO was never actually registered, we decided to adopt the term into OBI and replaced OBI:0002744 by newly assigned ID: OBI:0002744. Group: OBI molecular tracer OBI developer call, 3-12-12 https://github.com/obi-ontology/obi/issues/1135 molecular label A vacuum assisted biopsy can remove an area of abnormal cells from breast tissue. A biopsy performed with a needle augmented with a vacuum device. Damion Dooley VAB https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769667/ vacuum-assisted biopsy A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution. John Judkins PMC3297553 induced sputum specimen A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number. John Judkins https://en.wikipedia.org/wiki/Serial_passage https://www.merriam-webster.com/dictionary/passage passage process A data item that is about the sequence of environmental systems in each of which is grown an organism in a passage process. John Judkins https://en.wikipedia.org/wiki/Serial_passage https://www.merriam-webster.com/dictionary/passage passage history record Oxford Nanopore MinION Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. PERSON: Bonita Lam ONT MinION, MinION https://nanoporetech.com/products/minion Oxford Nanopore MinION Oxford Nanopore GridION Mk1 Nineteen libraries were constructed and sequenced on nineteen different R9.4 FlowCells using the GridION X5 sequencer A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individually. PERSON: Bonita Lam Oxford Nanopore GridION X5, GridION Mk1 https://nanoporetech.com/products/gridion Oxford Nanopore GridION Mk1 Oxford Nanopore PromethION Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome. A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. PERSON: Bonita Lam PromethION https://nanoporetech.com/products/promethion Oxford Nanopore PromethION Precision nuclear run-on and sequencing to detect Pol II initiation sites Bonita Lam PRO-CAP https://github.com/obi-ontology/obi/issues/1102 PRO-cap cDNA library cDNA library lacks the non-coding and regulatory elements found in genomic DNA A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription. Dan Berrios modified from Wikipedia cDNA library A categorical value specification in which the available categories were created with an explicit order. https://en.wikipedia.org/wiki/Ordinal_data provides references for follow-up, but more than one OBI developer has objected to "...whose levels have natural, ordered categories and the distances between those categories is not known..." Separate from that, an OBI mechanism for asserting the order of ordinal values specification levels with OWL has not been determined yet. Mark Andrew Miller, ORCID:0000-0001-9076-6066 Bjoern Peters in https://github.com/obi-ontology/obi/issues/862 https://github.com/obi-ontology/obi/issues/862 ordinal value specification A transcription profiling by RNA sequencing assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection. Michelle Giglio Rebecca Jackson Sebastian Duesing Suvarna Nadendla rRNA-deleted RNA sequencing assay rRNA-depleted RNA sequencing assay PMID:29556074 CFDE ribosomal RNA-depleted RNA sequencing assay A transcription profiling by RNA sequencing assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome. Michelle Giglio Rebecca Jackson Sebastian Duesing Suvarna Nadendla PMID:31450270 CFDE metatranscriptome profiling assay An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism. Michelle Giglio Rebecca Jackson Suvarna Nadendla lipidomic assay OBI metabolite profiling assay CFDE lipid profiling assay snATAC-seq can be used to dissect heterogeneity and delineate gene regulatory sequences in complex tissues, and uncover both the cell types and the regulatory elements in each cell type without prior knowledge. An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei. Mark Andrew Miller, ORCID:0000-0001-9076-6066 snATAC-seq http://www.biorxiv.org/content/early/2017/07/06/159137 https://github.com/obi-ontology/obi/issues/864 ENCODE single-nucleus ATAC-seq An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample. Michelle Giglio Rebecca Jackson Suvarna Nadendla 16S rRNA sequencing assay PMID:31450270 CFDE 16s ribosomal gene sequencing assay An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles. Mark Andrew Miller, ORCID:0000-0001-9076-6066 scATAC-seq http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html https://github.com/obi-ontology/obi/issues/864 ENCODE single-cell ATAC-seq A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome. Michelle Giglio Rebecca Jackson Suvarna Nadendla metaproteomic assay PMID:31450270 CFDE microbiome protein expression profiling assay An analyte assay to study presence, concentration, or amount of cytokines. Michelle Giglio Rebecca Jackson Suvarna Nadendla PMID:23603216 CFDE cytokine assay A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced. Michelle Giglio Rebecca Jackson Suvarna Nadendla PMID:29628929 PMID:31450270 CFDE amplicon sequencing assay A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample. Michelle Giglio Rebecca Jackson Suvarna Nadendla OBI:0002623 CFDE whole virome sequencing assay A genetic characteristics information that is about the number and appearance of chromosomes in the nucleus of an eukaryotic cell. Jie Zheng EFO_0004426 karyotype https://github.com/obi-ontology/obi/issues/1097 VEuPathDB karyotype information A karyotype information that is about the structural variation of partial genome rather than whole genome. Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1097 VEuPathDB partial karyotype information A karyotype information that is about the structural variation of the whole genome. Jie Zheng OBI group https://github.com/obi-ontology/obi/issues/1097 full karyotype information An ordinal value specification that indicates that either a) an analyte or mesaurand is present in an evaluant, or b) that the amount of analyte/measurand detected is over some predetermined threshold. Mark Andrew Miller, ORCID:0000-0001-9076-6066 LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 32 https://github.com/obi-ontology/obi/issues/1202 bump presence or over-threshold value specification Detection of SARS-CoV-2 IgG antibodies by an immunoassay method, such as enzyme-linked immunosorbent assay. This test is used in conjunction with SARS-CoV-2 IgA and IgM to aid in the diagnosis of COVID-19 and in the identification of individuals infected with SARS-CoV-2. An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest LOINC indicates that this class would not include flow cytometry or any technique that can determine the localization of an analyte, such as peroxidase immune staining or indirect immunofluorescence (IFA) Mark Andrew Miller, ORCID:0000-0001-9076-6066 IA immunoassay LOINC User's Guide, Version 2.68, PUBLISHED JUNE 2020, page 47 https://github.com/obi-ontology/obi/issues/1203 single-value binding of antibody with reporter to antigen assay A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter. PERSON: Matthew Diller platelet-poor plasma specimen A material component separation process in which (1) whole blood is first centrifuged to separate red blood cells from blood plasma, which forms the supernatant, and (2) the blood plasma is then centrifuged to separate platelets from the plasm. PERSON: Matthew Diller platelet-poor plasma preparation process A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by an algorithm in order to quantify the frequency of different cell populations of interest. Bjoern Peters CMI-PB https://github.com/obi-ontology/obi/issues/1226 cytometry analysis by automated gating A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by a human operator in order to quantify the frequency of different cell populations of interest. Bjoern Peters CMI-PB https://github.com/obi-ontology/obi/issues/1226 cytometry analysis by manual gating A specimen that is collected with a suctioning tube from the trachea. Asiyah Yu Lin ORCID:0000-0003-2620-0345 tracheal wash specimen PMID:25338241 tracheal aspirate specimen A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 https://seattlechildrenslab.testcatalog.org/catalogs/185/files/11633 mid-turbinate nasal swab specimen A specimen that is collected with a suctioning tube from the nasal cavity. Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal wash specimen nasopharyngeal aspirate Asiyah Yu Lin ORCID:0000-0003-2620-0345 nasal aspirate specimen A specimen that is collected with a suctioning tube from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract wash specimen Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract aspirate specimen A specimen that is derived from the upper respiratory tract Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 obsolete_upper respiratory specimen true A specimen that is derived from the lower respiratory tract. Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 lower respiratory tract specimen A specimen that is derived from the anterior nasal wall Asiyah Yu Lin ORCID:0000-0003-2620-0345 Asiyah Yu Lin ORCID:0000-0003-2620-0345 anterior nasal swab specimen Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue. Asiyah Yu Lin|ORCID:0000-0003-2620-0345 aspiration procedure https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C15631 aspiration specimen collection personal protective device Examples of PPE include respirators, gloves, aprons, fall protection, and full body suits, as well as head, eye and foot protection. PPE is equipment worn by a worker to minimize exposure to specific hazards. A device which is a wearable garment designed to protect the wearer's body from injury or infection. https://orcid.org/0000-0002-8844-9165 PPE personal protective equipment https://en.wikipedia.org/wiki/Personal_protective_equipment https://github.com/obi-ontology/obi/issues/1193 personal protective device face mask A systematic review on the efficacy of face coverings against respiratory viruses analyzed 19 randomized trials and concluded that use of face masks and respirators appeared to be protective in both health care and community settings A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles. https://orcid.org/0000-0002-8844-9165 face covering respirator Adapted from https://dictionary.cambridge.org/dictionary/english/face-mask https://github.com/obi-ontology/obi/issues/1193 face mask non-medical mask A non-medical mask may contain fabrics that are not regulated for use in surgical masks or respirators, or may not be designed to form a seal around the nose and mouth. A face mask not manufactured according to medical equipment standards. https://orcid.org/0000-0002-8844-9165 cloth mask https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html https://github.com/obi-ontology/obi/issues/1193 non-medical mask medical mask The finding of a much higher rate of infection in the cloth mask arm could be interpreted as harm caused by cloth masks, efficacy of medical masks, or most likely a combination of both. A face mask manufactured according to a recognized medical equipment standard. https://orcid.org/0000-0002-9578-0788 surgical mask https://www.canada.ca/en/public-health/services/diseases/2019-novel-coronavirus-infection/prevention-risks/about-non-medical-masks-face-coverings.html https://github.com/obi-ontology/obi/issues/1193 medical mask N95 respirator A face mask that meets the U.S. National Institute for Occupational Safety and Health (NIOSH) N95 classification of air filtration, meaning that it filters at least 95% of incoming airborne particles. https://orcid.org/0000-0002-8844-9165 N95 N95 face mask N95 facemask N95 respirator mask https://en.wikipedia.org/wiki/N95_mask https://github.com/obi-ontology/obi/issues/1193 N95 respirator face shield A personal protective device used to protect the wearer's entire face (or part of it) from hazards such as flying objects and road debris, chemical splashes, or alternately potentially infectious materials. https://orcid.org/0000-0002-8844-9165 faceshield splash shield https://en.wikipedia.org/wiki/Face_shield https://github.com/obi-ontology/obi/issues/1193 face shield patient gown A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff. https://orcid.org/0000-0002-8844-9165 hospital gown https://en.wikipedia.org/wiki/Patient_gown https://github.com/obi-ontology/obi/issues/1193 patient gown scrubs Examples consist of a short-sleeve V-necked shirt and drawstring pants or a short-sleeve calf-length dress, a tie-back or bouffant-style cap, a mask, a surgical gown, latex gloves, and supportive closed-toe shoes. A personal protective clothing item which is sterilized and which is worn by a health care professional. It can reference a shirt and pants or dress, and depending on medical protocol, may include a medical cap. https://orcid.org/0000-0002-8844-9165 scrub clothing item https://en.wikipedia.org/wiki/Scrubs_(clothing) https://github.com/obi-ontology/obi/issues/1193 scrubs reusable patient gown A patient gown intended to be reused after being laundered. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Patient_gown https://github.com/obi-ontology/obi/issues/1193 reusable patient gown disposable patient gown A patient gown intended for a single period of continuous use and then disposed of. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Patient_gown https://github.com/obi-ontology/obi/issues/1193 disposable patient gown medical gown A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional. https://orcid.org/0000-0002-8844-9165 hospital gown https://en.wikipedia.org/wiki/Medical_gown https://github.com/obi-ontology/obi/issues/1193 medical gown apron A garment which is worn over other clothing and covers mainly the front of the body. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Apron https://github.com/obi-ontology/obi/issues/1193 apron surgical gown A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures. https://orcid.org/0000-0002-8844-9165 OBI https://github.com/obi-ontology/obi/issues/1193 surgical gown personal protective glove A personal protective device which is a glove. https://orcid.org/0000-0002-8844-9165 OBI https://github.com/obi-ontology/obi/issues/1193 personal protective glove personal protective clothing item A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing. https://orcid.org/0000-0002-8844-9165 OBI https://github.com/obi-ontology/obi/issues/1193 personal protective clothing item laboratory coat A personal protective clothing item which is an overcoat worn by medical or laboratory professionals. https://orcid.org/0000-0002-8844-9165 white coat https://en.wikipedia.org/wiki/White_coat https://github.com/obi-ontology/obi/issues/1193 laboratory coat medical glove A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Medical_glove https://github.com/obi-ontology/obi/issues/1193 medical glove nitrile glove A personal protective glove which is made out of nitrile rubber. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Medical_glove https://github.com/obi-ontology/obi/issues/1193 nitrile glove transparent partition A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements. https://orcid.org/0000-0002-8844-9165 transparent partition https://ncceh.ca/content/blog/physical-barriers-covid-19-infection-prevention-and-control-commercial-settings https://github.com/obi-ontology/obi/issues/1193 transparent droplet barrier footwear cover A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants. https://orcid.org/0000-0002-8844-9165 boot cover shoe cover https://en.wiktionary.org/wiki/shoecover https://github.com/obi-ontology/obi/issues/1193 footwear cover disposable footwear cover A footwear cover which is designed for a single period of continuous use and then disposed of. https://orcid.org/0000-0002-8844-9165 OBI https://github.com/obi-ontology/obi/issues/1193 disposable footwear cover reusable footwear cover A footwear cover which is designed for repeated use. https://orcid.org/0000-0002-8844-9165 OBI https://github.com/obi-ontology/obi/issues/1193 reusable footwear cover surgical N95 respirator A N95 respirator which has been approved by the FDA as a surgical mask. https://orcid.org/0000-0002-8844-9165 healthcare respirator medical respirator surgical N95 surgical N95 respirator https://multimedia.3m.com/mws/media/1794572O/surgical-n95-vs-standard-n95-which-to-consider.pdf https://github.com/obi-ontology/obi/issues/1193 surgical N95 respirator protective coverall A personal protective clothing item which is a loose fitting coverall for ease of movement, with sleeves, full leggings and often a hood to cover the head. These can also include overshoe pieces to cover footwear and protect against contamination. https://orcid.org/0000-0002-8844-9165 https://www.safeopedia.com/definition/863/disposable-coveralls https://github.com/obi-ontology/obi/issues/1193 protective coverall protective sleeve A protective sleeve can be designed to provide protection from heat, welding spatter or hot metal, chemicals, sharp objects, paint or other liquids. A personal protective clothing item which is a protective cover worn over the arm. https://orcid.org/0000-0002-8844-9165 https://www.safeopedia.com/definition/974/protective-sleeves https://github.com/obi-ontology/obi/issues/1193 protective sleeve protective apron A personal protective clothing item which is an apron. https://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Apron https://github.com/obi-ontology/obi/issues/1193 protective apron medical cap A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp. https://orcid.org/0000-0002-8844-9165 bouffant cap bouffant hat medical bonnet scrub cap surgical hat https://en.wikipedia.org/wiki/Scrubs_(clothing) https://github.com/obi-ontology/obi/issues/1193 medical cap specimen collection device A device used to collect a specimen. https://orcid.org/0000-0002-8844-9165 specimen collection device chromatography vial A vial with cap and container material suited to optical, sanitary and handling requirements of chromatography. PERSON:Daniel Schober GROUP:<http://msi-ontology.sourceforge.net> http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117 chromatography vial specimen pad An absorbent pad and its accompanying container are designed to provide safe storage and transport to various degrees for diagnostic and clinical samples, infectious and hazardous materials, chemicals, pharmaceuticals and environmental samples. A sample collection device consisting of a soft flexible, absorbent pad usually made from natural material such as gauze or cotton, used to absorb specimen fluid or particulate matter. https://orcid.org/0000-0002-8844-9165 absorbant pad polysponge sample pad sampling sponge specimen sponge surface wipe swab Derived from NCIT sponge definition. specimen pad specimen collection swab stick A swab stick allows a worker to collect samples without touching the inside of the bag A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material. https://orcid.org/0000-0002-8844-9165 polyprobe sponge probe sponge stick sponge-stick https://medical-dictionary.thefreedictionary.com/swab specimen collection swab stick cotton swab A device which is a cotton pad mounted on one or both ends of a stick. https://orcid.org/0000-0002-8844-9165 Q-tip swab-sampler https://en.wikipedia.org/wiki/Cotton_swab cotton swab drag swab A specimen collection device consisting of a specimen pad made of sterile gauze which is aseptically attached to a pole by clips or to a string https://orcid.org/0000-0002-8844-9165 https://www.fda.gov/food/laboratory-methods-food/environmental-sampling-and-detection-salmonella-poultry-houses drag swab pre-moistened swab stick A specimen collection swab stick that is pre-moistened with liquid prior to sampling. https://orcid.org/0000-0002-8844-9165 pre-moistened swab stick surface wipe Surface sampling procedures involved the use of polyester wipes, swabs, contact slides (two types), and adhesive tapes; a gelatin filter was used to sample the air. A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces. https://orcid.org/0000-0002-8844-9165 https://www.science.gov/topicpages/s/surface+wipe+sampling.html surface wipe catheter A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body. https://orcid.org/0000-0002-8844-9165 http://purl.bioontology.org/ontology/MESH/D057785 catheter surveillance process An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. Chris Stoeckert Shane Babcock, OBI https://github.com/obi-ontology/obi/issues/1181 IDO, VEuPathDB surveillance process cluster study group role A cluster study group consisting of eight pregnant women who lived close enough to each other so that a community promoter could readily walk to each compound. A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. Chris Stoeckert, Brianna Lindsay cluster study arm ClinEpiDB cluster study group role compound study group role A compound study group consisting of geographically proximate households that share a common water source. A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol. Chris Stoeckert, Brianna Lindsay compound study arm ClinEpiDB compound study group role ultraviolet light source A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system. Person: Jie Zheng UV light source Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1200 VEuPathDB ultraviolet light source visible light source A light source that provides visible light for use in a distant area using a delivery system. Person: Jie Zheng Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1200 VEuPathDB visible light source solar light source A light source that light is produced from solar energy. Person: Chris Stoeckert Person: Jie Zheng Person: Chris Stoeckert Person: Jie Zheng https://github.com/obi-ontology/obi/issues/1200 VEuPathDB solar light source A live arthropod specimen collection process in which the arthropods are in the adult stage. John Judkins collection of adults MIRO:30000052 https://github.com/obi-ontology/obi/issues/1217 adult arthropod specimen collection process An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal. John Judkins animal biting catch MIRO:30000012 https://github.com/obi-ontology/obi/issues/1217 animal-biting arthropod specimen collection by aspiration An animal-biting arthropod specimen collection by aspiration that occurs outside a building. John Judkins animal biting catch - outdoors MIRO:30000014 https://github.com/obi-ontology/obi/issues/1217 animal-biting outdoor arthropod specimen collection by aspiration An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment. John Judkins aquatic environment catch MIRO:30000048 https://github.com/obi-ontology/obi/issues/1217 aquatic arthropod specimen collection process An arthropod specimen collection by aspiration that catches specimens resting inside an animal house. John Judkins animal shed resting catch MIRO:30000027 https://github.com/obi-ontology/obi/issues/1217 arthropod resting in animal house specimen collection by aspiration An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture. John Judkins outdoors shelter catch - artificial MIRO:30000026 https://github.com/obi-ontology/obi/issues/1217 arthropod resting outdoors on artificial support specimen collection by aspiration An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant. John Judkins outdoors shelter catch - natural MIRO:30000025 https://github.com/obi-ontology/obi/issues/1217 arthropod resting outdoors on natural support specimen collection by aspiration An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity. John Judkins outdoors shelter catch MIRO:30000024 https://github.com/obi-ontology/obi/issues/1217 arthropod resting outdoors specimen collection by aspiration A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container. John Judkins catch by aspiration MIRO:30000043 https://github.com/obi-ontology/obi/issues/1217 arthropod specimen collection by aspiration A specimen collection process that has the objective of collecting arthropods as specimens. John Judkins collection of arthropods field population catch MIRO:30000044 https://github.com/obi-ontology/obi/issues/1217 arthropod specimen collection process An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human. John Judkins man biting catch MIRO:30000017 https://github.com/obi-ontology/obi/issues/1217 human-biting arthropod specimen collection by aspiration An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building. John Judkins man biting catch - indoors MIRO:30000019 https://github.com/obi-ontology/obi/issues/1217 human-biting indoor arthropod specimen collection by aspiration An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building. John Judkins man biting catch - outdoors MIRO:30000018 https://github.com/obi-ontology/obi/issues/1217 human-biting outdoor arthropod specimen collection by aspiration A knockdown arthropod specimen collection process in which the pesticide is pyrethrum. John Judkins pyrethrum spray catch MIRO:30000023 https://github.com/obi-ontology/obi/issues/1217 knockdown arthropod specimen collection by pyrethrum spray An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized. John Judkins knockdown collection IRO:0000014 https://github.com/obi-ontology/obi/issues/1217 knockdown arthropod specimen collection process An arthropod specimen collection process meant to collect live specimens. John Judkins catch of live specimens MIRO:30000044 VSMO:0001445 https://github.com/obi-ontology/obi/issues/1217 live arthropod specimen collection process A device designed to catch arthropods. John Judkins MIRO:30000011 https://github.com/obi-ontology/obi/issues/1217 arthropod trap An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected. John Judkins IRO:0000005 https://github.com/obi-ontology/obi/issues/1217 artificial pit shelter An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal. John Judkins https://github.com/obi-ontology/obi/issues/1217 baited net trap An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container. John Judkins IRO:0000017 https://github.com/obi-ontology/obi/issues/1217 barrier trap A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods. John Judkins IRO:0000143 https://github.com/obi-ontology/obi/issues/1217 BG-Counter An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current. John Judkins IRO:0000028 VSMO:0001906 https://github.com/obi-ontology/obi/issues/1217 BG-Sentinel trap A light trap that is designed similarly to the New Jersey trap—in that it uses motorized suction and light attractant—and is powered by a six-volt battery. This trap is also designed to be lightweight and operate in environments in which electricity may be scarce. John Judkins CDC light trap IRO:0000163 https://github.com/obi-ontology/obi/issues/1217 Centers for Disease Control and Prevention light trap A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan. John Judkins dipper for immatures VSMO:0001479 https://github.com/obi-ontology/obi/issues/1217 dipper for arthropod immatures A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods. John Judkins EVS trap IRO:0000029 VSMO:0001295 https://github.com/obi-ontology/obi/issues/1217 encephalitis virus surveillance trap An arthropod trap that is designed to collect gravid female arthropods or their eggs. John Judkins IRO:0000030 https://github.com/obi-ontology/obi/issues/1217 gravid trap An arthropod trap that uses light as an attractant. John Judkins MIRO:30000065 https://github.com/obi-ontology/obi/issues/1217 light trap A light trap designed to be placed inside a building. John Judkins indoor light trap MIRO:30000009 https://github.com/obi-ontology/obi/issues/1217 light trap for indoor use A light trap designed to be placed outside a building. John Judkins outdoor light trap MIRO:30000010 https://github.com/obi-ontology/obi/issues/1217 light trap for outdoor use An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. John Judkins IRO:0000022 https://github.com/obi-ontology/obi/issues/1217 Mosquito Magnet Pro trap A gravid trap consisting of an arthropod attractant and adhesive surface. John Judkins IRO:0000140 https://github.com/obi-ontology/obi/issues/1217 MosquiTRAP A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant. John Judkins New Jersey trap IRO:0000031 https://github.com/obi-ontology/obi/issues/1217 New Jersey light trap A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter. John Judkins OVI light-suction trap IRO:0000154 Parasites Vectors 8, 239 (2015) https://github.com/obi-ontology/obi/issues/1217 Onderstepoort Veterinary Institute light-suction trap An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building. John Judkins outlet window trap MIRO:30000020 https://github.com/obi-ontology/obi/issues/1217 outlet window trap An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females. John Judkins oviposition trap MIRO:30000016 VSMO:0001501 https://github.com/obi-ontology/obi/issues/1217 ovitrap An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity. John Judkins https://github.com/obi-ontology/obi/issues/1217 resting arthropod trap An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. John Judkins resting box catch IRO:0000021 https://github.com/obi-ontology/obi/issues/1217 resting box trap An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity (not actively seeking a host). John Judkins resting bucket catch IRO:0000141 https://github.com/obi-ontology/obi/issues/1217 resting bucket An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap. John Judkins shannon trap catch IRO:0000191 https://github.com/obi-ontology/obi/issues/1217 Shannon trap An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected. John Judkins sticky resting bucket catch IRO:0000142 https://github.com/obi-ontology/obi/issues/1217 sticky resting bucket An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive. John Judkins sticky trap catch IRO:0000128 https://github.com/obi-ontology/obi/issues/1217 sticky trap population based design A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment. Chris Stoeckert https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design https://github.com/obi-ontology/obi/issues/1090 population based design A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:http://lincsportal.ccs.miami.edu/beta/assays/1 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS fluorescence imaging-based apoptosis assay A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells. Michelle Giglio Rebecca Jackson Suvarna Nadendla fluorescence imaging-based cell count assay url:http://lincsportal.ccs.miami.edu/beta/assays/31 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS fluorescence imaging-based cell proliferation assay A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:http://lincsportal.ccs.miami.edu/beta/assays/10 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS fluorescence imaging-based cell cycle state assay A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:http://lincsportal.ccs.miami.edu/beta/assays/27 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS fluorescence imaging-based cell viability assay A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:http://lincsportal.ccs.miami.edu/beta/assays/7 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS fluorescence imaging-based drug synergy assay A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology. Michelle Giglio Rebecca Jackson Suvarna Nadendla CFDE Michelle Giglio Suvarna Nadendla https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS fluorescence imaging-based cell morphology assay A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:http://lincsportal.ccs.miami.edu/beta/assays/8 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS fluorescence imaging multiplex cytological profiling A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc. Michelle Giglio Rebecca Jackson Suvarna Nadendla CFDE Michelle Giglio Suvarna Nadendla https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS protein state assay A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:http://lincsportal.ccs.miami.edu/beta/assays/15 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS fluorescence imaging-based protein phosphorylation state assay A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states. Michelle Giglio Rebecca Jackson Suvarna Nadendla CFDE Michelle Giglio Suvarna Nadendla https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS mass spectrometry-based protein state assay A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations. Michelle Giglio Rebecca Jackson Suvarna Nadendla P100 phosphoprotein quantification assay PMID:26912667 PMID:29655704 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications. Michelle Giglio Rebecca Jackson Suvarna Nadendla RPLA assay RPPA assay reverse phase lysate array profiling assay PMID: 17041095 PMID:31820393 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS reverse phase protein array profiling assay A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides. Michelle Giglio Rebecca Jackson Suvarna Nadendla sequential window acquisition of all theoretical mass spectra protein profiling assay PMID:30104418 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS SWATH-MS protein profiling assay A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins. Michelle Giglio Rebecca Jackson Suvarna Nadendla PMID:12713048 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS tandem mass tag mass spectrometry assay A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression. Michelle Giglio Rebecca Jackson Suvarna Nadendla CFDE Michelle Giglio Suvarna Nadendla https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS fluorescence imaging-based reporter gene assay A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin. Michelle Giglio Rebecca Jackson Suvarna Nadendla GCP global chromatin epigenetic profiling global chromatin profiling PMID:25448295 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS global chromatin profiling by mass spectrometry assay A type of assay that identifies compounds that inhibit the activity of kinases. Michelle Giglio Rebecca Jackson Suvarna Nadendla CFDE Michelle Giglio Suvarna Nadendla https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS kinase inhibitor assay A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:https://www.discoverx.com/technologies-platforms/competitive-binding-technology/kinomescan-technology-platform https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS KINOMEscan assay A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:https://www.kinativ.com/technology.html https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS KiNativ assay A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence. Michelle Giglio Rebecca Jackson Suvarna Nadendla L1000 mRNA profiling assay PMID:29195078 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS landmark transcript profiling assay A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity. Michelle Giglio Rebecca Jackson Suvarna Nadendla MEMA assay PMID:29199020 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS microenvironment microarray assay A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose. Michelle Giglio Rebecca Jackson Suvarna Nadendla PMID:28092050 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS microwestern meso-scale quantitative western blot assay A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples. Michelle Giglio Rebecca Jackson Suvarna Nadendla positive/negative ion switching metabolomic assay PMID:22498707 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS positive/negative ion switching metabolite profiling assay A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation. Michelle Giglio Rebecca Jackson Suvarna Nadendla PMID:27925668 PMID:29993362 https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS cyclic immunofluoroescence assay A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:https://www.bio-rad.com/en-us/applications-technologies/multiplex-immunoassays?ID=LUSM0E8UU https://github.com/obi-ontology/obi/issues/1243 CFDE-LINCS multiplex bead-based protein state immunoassay A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea. John Judkins ORCID:0000-0001-6595-0902 https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 endotracheal tube specimen A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube. John Judkins ORCID:0000-0001-6595-0902 https://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-019-0926-3 endotracheal aspirate specimen When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being analyzed is the input protein sequence start site. The position of the first amino acid in a protein sequence being analyzed (input protein sequence). Emma Griffiths input protein start query protein start site Emma Griffiths input protein sequence start site When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence being analyzed is the input protein sequence stop site. The position of the last amino acid in a protein sequence being analyzed (input protein sequence). Emma Griffiths input protein stop query protein stop site Emma Griffiths input protein sequence stop site When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence being analyzed is the input gene sequence start site. The position of the first nucleotide in a gene sequence being analyzed (input gene sequence). Emma Griffiths input gene start query gene start site Emma Griffiths input gene sequence start site When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence being analyzed is the input gene sequence stop site. The position of the last nucelotide in a gene sequence being analyzed (input gene sequence). Emma Griffiths input gene stop query gene stop site Emma Griffiths input gene sequence stop site When a new genome is sequenced, the start sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The first amino acid of a protein sequence being used for comparison is the reference protein sequence start site. The position of the first amino acid in a reference protein sequence (sequence being used for comparison). Emma Griffiths reference protein start subject protein start site Emma Griffiths reference protein sequence start site When a new genome is sequenced, the termination sites of proteins are identified by comparing the new sequence to that of a reference sequence in a database. The last amino acid of a protein sequence used for comparison is the reference protein sequence stop site. The position of the last amino acid in a reference protein sequence (sequence being used for comparison). Emma Griffiths reference protein stop subject protein stop site Emma Griffiths reference protein sequence stop site When a new genome is sequenced, the start sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The first nucelotide of a gene sequence used for comparison is the reference gene sequence start site. The position of the first nucleotide in a reference gene sequence (sequence being used for comparison). Emma Griffiths reference gene start subject gene start site Emma Griffiths reference gene sequence start site When a new genome is sequenced, the termination sites of genes are identified by comparing the new sequence to that of a reference sequence in a database. The last nucelotide of a gene sequence used for comparison is the reference gene sequence stop site. The position of the last nucelotide in a reference sequence (sequence being used for comparison). Emma Griffiths reference gene stop subject gene stop site Emma Griffiths reference gene sequence stop site altitude measurement datum A length measurement datum between a point at sea or ground level and some point above it. Chris Stoeckert Adapted from https://www.merriam-webster.com/dictionary/altitude altitude measurement datum PMID:29979818 Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA. A Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest. Bonita Lam cHi-C PMID:29979818 https://github.com/obi-ontology/obi/issues/1251 capture Hi-C assay An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity. Alexander D. Bartnik, ORCID:0000-0001-9676-7377 Alexander D. Diehl, ORCID:0000-0001-9990-8331 Lauren M. Wishnie, ORCID:0000-0002-7245-3450 Lucas M. Serra, ORCID:0000-0002-2104-0568 Mackenzie T. Smith, ORCID:0000-0002-9821-4132 Rebecca Jackson William D. Duncan, ORCID:0000-0001-9625-1899 MRI url:https://en.wikipedia.org/wiki/Magnetic_resonance_imaging https://github.com/obi-ontology/obi/issues/1290 magnetic resonance imaging assay An imaging assay that uses a series of X-ray images to produce information about the interior structure and composition of an input material entity. Rebecca Jackson CAT scan CT scan computed tomography scan url:https://www.mayoclinic.org/tests-procedures/ct-scan/about/pac-20393675 https://github.com/obi-ontology/obi/issues/1290 computed tomography imaging assay An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity. Rebecca Jackson PET scan positron emission tomography scan url:https://en.wikipedia.org/wiki/Positron_emission_tomography https://github.com/obi-ontology/obi/issues/1290 positron emission tomography imaging assay duration of specimen collection Specimen collection duration of 3 nights that a trap is set out for collection of mosquitoes. Urine collected over a 24 hour period of specimen collection duration. A time measurement datum that is the count of collection cycles over which a specimen collection process occurs. specimen collection duration VEuPathDB specimen collection duration material supplier A person or organization that provides material supplies to other people or organizations. Rebecca Jackson https://github.com/obi-ontology/obi/issues/1289 material supplier A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample. Rebecca Jackson TCR repertoire sequencing assay bulk TCR assay doi:10.1186/s12896-017-0379-9 https://github.com/obi-ontology/obi/issues/1307 T cell receptor repertoire sequencing assay A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample. Rebecca Jackson Antibody repertoire sequencing assay BCR repertoire sequencing assay bulk BCR assay doi:10.1186/s12896-017-0379-9 https://github.com/obi-ontology/obi/issues/1307 B cell receptor repertoire sequencing assay prevalence of pathogen in specimens prevalence of Plasmodium falciparum in Mosquito samples assayed by PCR A data item that is the frequency of detection of a specified pathogenic organism in collected specimens. Chris Stoeckert prevalence of pathogen VEuPathDB prevalence of pathogen in specimens prevalence of blood meal specimens from a host organism prevalence of blood meal host organism in specimens measured as % of blood meal specimens collected from mosquitoes that had human blood as a meal. A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens. Chris Stoeckert host blood index VEuPathDB prevalence of blood meal specimens from a host organism presence of blood from host organism in blood meal specimen presence of blood meal host organism indicated by boolean values of yes or no. A data item that indicates whether blood in a blood meal specimen came from a specified host organism. Chris Stoeckert presence of blood meal host organism VEuPathDB presence of blood from host organism in blood meal specimen blood meal source organism An organism that is the source of a blood meal. Chris Stoeckert blood meal host organism VEuPathDB blood meal source organism blood meal source role A mosquito feeds on a human whereby the human acquires the blood meal source role for the mosquito blood meal. A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism. Will deprecate this term in VEuPathDB ontology once in OBI. Chris Stoeckert http://purl.obolibrary.org/obo/EUPATH_0000791 blood meal source role A role of a material entity realized in drawing an arthropod in the direction of the material. John Judkins attractant IRO:0000034 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB arthropod attractor role An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 VEuPathDB arthropod collection process with automated identification An arthropod specimen collection process that has the objective of collecting gravid female arthropods. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 VEuPathDB gravid female arthropod specimen collection process An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity. John Judkins VSMO:0000514 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB resting flight-capable arthropod specimen collection process An arthropod specimen collection by aspiration that occurs in the daytime. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1302 VEuPathDB daytime arthropod specimen collection by aspiration An arthropod specimen collection by aspiration that catches specimens resting inside a human house. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB arthropod resting in human house specimen collection by aspiration An arthropod specimen collection process that occurs while the arthropods land on a surface. John Judkins collection of landing insects VSMO:0001457 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB landing arthropod specimen collection process An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB flying adult arthropod collection process by passive interception A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity. John Judkins VSMO:0001355 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB device for collection of resting adult arthropods A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net. John Judkins https://github.com/obi-ontology/obi/issues/1302 VEuPathDB well net for arthropod immatures An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller. John Judkins trap containing small non-human animal bait VSMO:0001595 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB arthropod trap containing small non-human animal bait An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage. John Judkins American Midland Naturalist, Vol. 97, No. 2 (Apr., 1977), pp. 381-389 VSMO:0001352 https://github.com/obi-ontology/obi/issues/1302 VEuPathDB trap for emerging adult arthropods An assay that measures ferritin James A. Overton, ORCID:0000-0001-5139-5557 OBI ferritin assay An assay that measures fibrinogen James A. Overton, ORCID:0000-0001-5139-5558 OBI fibrinogen assay An analyte assay that measures the abundance of iron James A. Overton, ORCID:0000-0001-5139-5559 OBI iron assay An analyte assay that measures the abundance of ionized calcium James A. Overton, ORCID:0000-0001-5139-5561 OBI ionized calcium assay An analyte assay that measures the abundance of transferrin James A. Overton, ORCID:0000-0001-5139-5562 OBI transferrin assay An analyte assay that measures the abundance of uric acid James A. Overton, ORCID:0000-0001-5139-5563 OBI uric acid assay An analyte assay that measures the abundance of globulin James A. Overton, ORCID:0000-0001-5139-5564 OBI globulin assay A cytometry assay that measures the abundance and/or characteristics of myelocytes James A. Overton, ORCID:0000-0001-5139-5565 OBI myelocyte assay A cytometry assay that measures the abundance and/or characteristics of metamyelocytes James A. Overton, ORCID:0000-0001-5139-5566 OBI metamyelocyte assay A cytometry assay that measures the proportion of red blood cells James A. Overton, ORCID:0000-0001-5139-5567 OBI hematocrit assay A cytometry assay that measures the abundance and/or characteristics of promyelocytes James A. Overton, ORCID:0000-0001-5139-5568 OBI promyelocyte assay A cytometry assay that measures the abundance and/or characteristics of basophils James A. Overton, ORCID:0000-0001-5139-5569 OBI basophil assay A cytometry assay that measures the abundance and/or characteristics of neutrophils James A. Overton, ORCID:0000-0001-5139-5570 OBI neutrophil assay A cytometry assay that measures the abundance and/or characteristics of eosinophils James A. Overton, ORCID:0000-0001-5139-5571 OBI eosinophil assay A cytometry assay that measures the abundance and/or characteristics of lymphocytes James A. Overton, ORCID:0000-0001-5139-5572 OBI lymphocyte assay A cytometry assay that measures the abundance and/or characteristics of monocytes James A. Overton, ORCID:0000-0001-5139-5573 OBI monocyte assay A cytometry assay that measures the abundance and/or characteristics of reticulocytes James A. Overton, ORCID:0000-0001-5139-5574 OBI reticulocyte assay A cytometry assay that measures the abundance and/or characteristics of macrophages James A. Overton, ORCID:0000-0001-5139-5577 OBI macrophage assay A cytometry assay that measures the abundance and/or characteristics of platelets James A. Overton, ORCID:0000-0001-5139-5578 OBI platelet assay barcode target locus role An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR. Chris Stoeckert https://orcid.org/0000-0002-5714-991X VEuPathDB https://github.com/obi-ontology/obi/issues/1325 barcode target locus role oligonucleotide primer set A processed material that consists of oligonucleotides that bear a primer role. Chris Stoeckert https://orcid.org/0000-0002-5714-991X VEuPathDB https://github.com/obi-ontology/obi/issues/1325 oligonucleotide primer set A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores. John Judkins TaqMan MIRO:20000102 https://github.com/obi-ontology/obi/issues/1320 fluorogenic PCR assay genotyping by PCR assay to identify microsatellites, chromosomal inversions and targeted assays of known resistance loci. A genotyping assay that uses polymerase chain reaction. Chris Stoeckert, ORCID:0000-0002-5714-991X Jie Zheng, ORCID:0000-0002-2999-0103 VEuPathDB https://github.com/obi-ontology/obi/issues/1348 VEuPathDB genotyping by PCR assay A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing. Michelle Giglio Rebecca Jackson Suvarna Nadendla CUT&RUN assay url:https://elifesciences.org/articles/21856 https://github.com/obi-ontology/obi/issues/1192 bonitalam cleavage under targets and release using nuclease assay A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing. Michelle Giglio Rebecca Jackson Suvarna Nadendla CUT&Tag assay url:https://www.nature.com/articles/s41467-019-09982-5 https://github.com/obi-ontology/obi/issues/1192 bonitalam cleavage under targets and tagmentation Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale. A physical examination of an organism that has the objective to determine the severity of coma in a patient. John Judkins https://github.com/obi-ontology/obi/issues/1357 John Judkins coma severity assay An assay that detects Plasmodium gametocytes in a specimen. Chris Stoeckert Jie Zheng John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 Plasmodium gametocyte detection assay An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood. Chris Stoeckert Jie Zheng malaria rapid diagnosis test VEuPathDB https://github.com/obi-ontology/obi/issues/1322 malaria rapid diagnosis assay An assay that detects parasite in a specimen. Chris Stoeckert Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1322 parasite detection assay An organism detection assay that detects microorganisms in a feces specimen. John Judkins stool test for microorganisms VEuPathDB https://github.com/obi-ontology/obi/issues/1322 feces microbiology assay An assay that has a blood specimen as evaulant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 blood assay A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 falcivax rapid diagnostic test A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 optimal-IT rapid diagnostic test An assay that has a urine specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 urine assay A parasite detection by PCR assay that identifies the species of parasite. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1322 parasite species identification by PCR assay A parasite detection assay that uses PCR. Chris Stoeckert Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1322 parasite detection by PCR assay Jonsson developed a free-standing window trap consisting of a 16 x 20-cm perspex box, 16 cm high and divided in the middle by a 20 x 36-cm sheet of perspex (window). The two compartments of the box are filled to a depth of about 12 cm with 4-6% formalin containing a few drops of detergent; in winter ethylene glycol can be added to prevent freezing. One or two holes drilled in one side of the box at 12 cm and covered with fine netting prevent the trap overflowing after heavy rain. Traps are mounted on aluminium poles. Flying insects on hitting the transparent vertical plastic window fall into the formalin. The window trap may catch vectors that are seeking a host or moving for other purposes. [ISBN:9781402066658] An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die. VEuPathDB VSMO:0001649 free-standing window trap A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin. VEuPathDB BG-lure IRO:0001060 BG-lure scent dispenser A device that consists of a network of mesh and is designed to capture adult arthropods. VEuPathDB VSMO:0001522 hand-held sweep net The original trap CDC gravid trap (or gravid trap of Reiter) consists of a 3 inch diameter PVC inlet tube housing a 6 V motor, as used in CDC traps, on which is mounted a four-bladed 3 inch counter-clockwise fan. The inlet tube is clamped between two vertical wooden boards that fit over a black plastic box (18.5 x 14.0 x 6.5 inches). A plastic 12 inch long PVC chimney slots into the upper end of the inlet tube. The top half consists of three struts that fit into and support a netting collecting bag. For this the middle of the collecting bag is reinforced with a circular patch of denim cloth. The oviposition attractant is made by adding 1 lb of hay and 1 oz each of dried brewer's yeast and lactalbumen powder to 30 gallons of tap water. This infusion is allowed to mature for 5 days. This original gravid mosquito trap of Reiter suffers from certain limitations, namely up to 10% of the catch of adults is damaged by passing through the fan blades, and adults tend to die of desiccation. [ISBN:9781402066658] A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan. VEuPathDB CDC gravid trap VSMO:0001510 Centers for Disease Control and Prevention gravid trap An arthropod specimen collection process in which the arthropods are in the embryo stage. VEuPath collection of eggs MIRO:30000049 https://github.com/obi-ontology/obi/issues/1322 egg specimen collection process An arthropod specimen collection process in which the arthropods are in the larval stage. VEuPath collection of larvae MIRO:30000022 https://github.com/obi-ontology/obi/issues/1322 larval specimen collection process An arthropod specimen collection process in which the arthropods are in the pupal stage. VEuPath collection of pupae MIRO:30000050 https://github.com/obi-ontology/obi/issues/1322 pupal specimen collection process A blood specimen that is located in a vacutainer. John Judkins Vacutainer sample VEuPathDB blood specimen in vacutainer A blood specimen that is located on a filter paper. Chris Stoeckert Jie Zheng Filter paper sample Penn Group blood specimen on filter paper A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads. John Judkins VEuPathDB proportion mapped reads antibiotic administration process Administering substance in vivo where an antibiotic substance is administered to a living organism. Chris Stoeckert Cristian Cocos Jie Zheng Penn Group antibiotic administration process A data item that is about resistance to an insecticide. John Judkins VEuPathDB insecticide resistance datum A data item that is the specified output of an organism detection assay. John Judkins VEuPathDB organism detection datum A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection. Easting and northing coordinates are commonly measured in meters from a horizontal datum. John Judkins https://en.wikipedia.org/wiki/Grid_reference_system easting coordinate measurement datum A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection. Easting and northing coordinates are commonly measured in meters from a horizontal datum. John Judkins https://en.wikipedia.org/wiki/Grid_reference_system northing coordinate measurement datum Organization that undertakes a clinical study at some point in time. Chris Stoeckert Cristian Cocos Jie Zheng Penn Group clinical study center A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial. John Judkins VEuPathDB sequencing protocol A protocol that specifies processes to fulfill a specimen collection objective. John Judkins VEuPathDB specimen collection protocol A symbol that denotes a participant under investigation. John Judkins VEuPathDB participant identifier A temperature measurement datum that is about an axilla. John Judkins VEuPathDB axillary temperature measurement datum A temperature measurement datum that is about an organism. Chris Stoeckert Jie Zheng Penn Group organismal body temperature measurement datum A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized. John Judkins https://en.wikipedia.org/wiki/Common_name common name of organism An age since birth measurement datum at the time of subject enrollment. Jie Zheng Penn Group age since birth at time of enrollment An age since birth measurement datum at the time of a clinical visit. Chris Stoeckert Grant Dorsey Jie Zheng Shon Cade Penn Group age since birth at time of visit A data item that is about a collection of insects. John Judkins entomological measurement datum VEuPathDB entomological data item A scalar measurement datum that is the result of measuring temperature. John Judkins VEuPathDB temperature measurement datum An assay that detects body temperature of an organism. Chris Stoeckert Jie Zheng VEuPathDB https://github.com/obi-ontology/obi/issues/1322 organismal body temperature measurement assay extraction date A time measurement datum that specifies when some material was extracted from an input material. Chris Stoeckert, ORCID: 0000-0002-5714-991X FLU, VEuPathDB https://github.com/obi-ontology/obi/issues/1286 extraction date extraction duration time A time measurement datum that is the result of measuring the duration of an extraction process. Chris Stoeckert, ORCID: 0000-0002-5714-991X Meredith Keybl, Shane Babcock https://github.com/obi-ontology/obi/issues/1286 extraction duration time specimen collection time post disease onset A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host. Chris Stoeckert, ORCID: 0000-0002-5714-991X GROUP:FLU, Shane Babcock https://github.com/obi-ontology/obi/issues/1286 specimen collection time post disease onset specimen collection time post infection A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts. Chris Stoeckert, ORCID: 0000-0002-5714-991X VEuPathDB, EUPATH:0000613 https://github.com/obi-ontology/obi/issues/1286 specimen collection time post infection laboratory postal address A postal address used as a directive to deliver something to a laboratory. Chris Stoeckert, ORCID: 0000-0002-5714-991X laboratory address GROUP:FLU, Shane Babcock https://github.com/obi-ontology/obi/issues/1286 laboratory postal address laboratory-based population Refers to whether the mosquitoes used in the analysis of insecticide resistance were collected from an established strain or any other population kept in a laboratory under controlled conditions. (per MIRO_30000033) A population where the collection of individuals is located and maintained in a laboratory, research, or production facility. Chris Stoeckert, ORCID: 0000-0002-5714-991X VEuPathDB https://github.com/obi-ontology/obi/issues/1370 laboratory-based population A fluorescence detection assay in which the light that is naturally emitted by a sample is visualized after excitation of the sample with light at a suitable wavelength. Michelle Giglio Rebecca Jackson Suvarna Nadendla intrinsic fluorescence assay PMID:25578980 url:https://en.wikipedia.org/wiki/Autofluorescence https://github.com/obi-ontology/obi/issues/1393 CFDE autofluorescence assay An autofluorescence assay in which the light that is naturally emitted by a sample is visualized via microscopy after excitation of the sample with light at a suitable wavelength. Michelle Giglio Rebecca Jackson Suvarna Nadendla PMID:25578980 url:https://en.wikipedia.org/wiki/Autofluorescence https://github.com/obi-ontology/obi/issues/1394 CFDE autofluorescence microscopy assay An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. Michelle Giglio Rebecca Jackson Suvarna Nadendla bulk ATAC-seq PMID:24097267 https://github.com/obi-ontology/obi/issues/1395 CFDE bulk assay for transposase-accessible chromatin using sequencing A transcription profiling by RNA sequencing assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. Michelle Giglio Rebecca Jackson Sebastian Duesing Suvarna Nadendla url:https://www.biostars.org/p/458516/ https://github.com/obi-ontology/obi/issues/1396 CFDE bulk RNA-seq assay An imaging assay in which multiple cycles consisting of fluorescent labeling, imaging, and fluorophor deactivation are used to detect multiple proteins and their locations in a given sample of tissues or cells. Michelle Giglio Rebecca Jackson Suvarna Nadendla PMID:29993362 https://github.com/obi-ontology/obi/issues/1397 CFDE multiplexed fluorescent antibody imaging assay A multiplexed fluorescent antibody imaging assay that involves an iterative staining, imaging and dye inactivation workflow for over 60 biomarkers on a single fixed tissue section. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:https://cancerres.aacrjournals.org/content/80/16_Supplement/1448 url:https://www.cytivalifesciences.co.kr/wp-content/uploads/2020/07/Cell-DIVE-Tech-Info-Sheet-CY11898-09Apr20-DF.pdf https://github.com/obi-ontology/obi/issues/1398 CFDE Cell DIVE multiplexed imaging assay A multiplexed fluorescent antibody imaging assay that involves a highly multiplexed analysis of up to 40 proteins in a tissue using cyclic detection of DNA-indexed antibody panels. Michelle Giglio Rebecca Jackson Suvarna Nadendla CODEX url:https://www.scilifelab.se/facilities/co-detection-by-indexing-codex/ https://github.com/obi-ontology/obi/issues/1399 CFDE co-detection by indexing assay An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences. Michelle Giglio Rebecca Jackson Suvarna Nadendla FISH url:https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization https://github.com/obi-ontology/obi/issues/1400 CFDE fluorescence in-situ hybridization assay A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types. Michelle Giglio Rebecca Jackson Suvarna Nadendla DARTFISH url:http://genome-tech.ucsd.edu/ZhangLab/index.php/data/tech-dev/ url:http://www.weizmann.ac.il/conferences/SCG2015/sites/conferences.SCG2015/files/scg_2015_abstractbook_online_version.pdf url:https://escholarship.org/uc/item/5bq3128f https://github.com/obi-ontology/obi/issues/1401 CFDE decoding amplified targeted transcripts with fluorescence in situ hybridization assay A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. The sample is then ablated with a laser and the labeled material is detected by cytometry time of flight mass spectrometry. Michelle Giglio Rebecca Jackson Suvarna Nadendla IMC imaging CyTOF PMID:31798587 https://github.com/obi-ontology/obi/issues/1403 CFDE imaging mass cytometry assay A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance. Michelle Giglio Rebecca Jackson Suvarna Nadendla LC-MS CHMO:0000524 https://github.com/obi-ontology/obi/issues/1404 CFDE liquid chromatography mass spectrometry assay A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/light-sheet-fluorescence-microscopy https://github.com/obi-ontology/obi/issues/1405 CFDE lightsheet fluorescence microscopy assay A mass spectrometry assay that involves collection of spatially resolved mass spectra of a sample during microscopy where a pulse laser is used to produce both ionisation and vaporization. The sample is held in a matrix (such as dihydrobenzoic acid) to protect it from direct laser illumination and to separate the sample molecules. The spectra are used to visualise the spatial distribution of biomolecules by their molecular masses. Michelle Giglio Rebecca Jackson Suvarna Nadendla MALDI-IMS url:http://purl.obolibrary.org/obo/CHMO_0000054 https://github.com/obi-ontology/obi/issues/1406 CFDE matrix assisted laser desorption ionization imaging mass spectrometry assay A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. A primary ion beam is ued to rasterize sections under vacuum, releasing showers of secondary ions detected by cytometry time of flight mass spectrometry. Michelle Giglio Rebecca Jackson Suvarna Nadendla MIBI url:https://www.nature.com/articles/s41374-020-0417-4 https://github.com/obi-ontology/obi/issues/1407 CFDE multiplexed ion beam imaging assay A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray. Michelle Giglio Rebecca Jackson Suvarna Nadendla NanoDESI url:https://pubmed.ncbi.nlm.nih.gov/20593081/ https://github.com/obi-ontology/obi/issues/1408 CFDE nanospray desorption electrospray ionization assay A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the global protein expression. Michelle Giglio Rebecca Jackson Suvarna Nadendla NanoPOTS url:https://www.emsl.pnnl.gov/science/related-instrument/nanodroplet-processing-in-one-pot-for-trace-samples--nanopots-/1806 https://github.com/obi-ontology/obi/issues/1409 CFDE nanodroplet processing in one pot for trace samples assay A histological assay which is used on tissue samples to demonstrate the presence of carbohydrates and carbohydrate compounds such as polysaccharides, mucin, glycogen, or fungal cell wall components. Michelle Giglio Rebecca Jackson Suvarna Nadendla PAS staining url:https://microbenotes.com/periodic-acid-schiff-pas-staining/ https://github.com/obi-ontology/obi/issues/1410 CFDE periodic acid-Schiff staining assay An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation. Michelle Giglio Rebecca Jackson Suvarna Nadendla sciATACseq url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158300/ https://github.com/obi-ontology/obi/issues/1411 CFDE single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing A single-cell transcription profiling by RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation. Michelle Giglio Rebecca Jackson Suvarna Nadendla sci-RNA-seq sciRNAseq url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894354/ https://github.com/obi-ontology/obi/issues/1412 CFDE single-cell combinatorial indexing RNA sequencing assay A fluorescence in-situ hybridization assay that involves ultra-resolution imaging of cell activity by targetting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved. Michelle Giglio Rebecca Jackson Suvarna Nadendla seqFISH url:https://spatial.caltech.edu/seqfish/ https://github.com/obi-ontology/obi/issues/1413 CFDE sequential fluorescence in-situ hybridization assay A transcription profiling by RNA sequencing assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing. Michelle Giglio Rebecca Jackson Suvarna Nadendla url:https://science.sciencemag.org/content/363/6434/1463 https://github.com/obi-ontology/obi/issues/1414 CFDE slide-seq assay An assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs. Michelle Giglio Rebecca Jackson Suvarna Nadendla SNARE-seq SNAREseq url:https://www.nature.com/articles/s41587-019-0290-0 https://github.com/obi-ontology/obi/issues/1416 CFDE single-nucleus chromatin accessibility and mRNA expression sequencing assay A RNA-seq assay that is used for profiling gene expression in individual nuclei with optimized next generation sequencing (NGS) technologies. This allows the RNA-seq profiling of cell types that are more vulnerable to the tissue dissociation process, and that are therefore underrepresented in the final data set in single cell sequencing. Michelle Giglio Rebecca Jackson Suvarna Nadendla sNuc-seq single nuclei RNA sequencing snRNA-seq EFO:0009809 url:https://www.biocompare.com/Editorial-Articles/557506-Advantages-of-Single-Nucleus-RNA-Sequencing/ https://github.com/obi-ontology/obi/issues/1415 CFDE obsolete single-nucleus RNA sequencing assay true A mass spectrometry assay combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determination of compounds. Michelle Giglio Rebecca Jackson Suvarna Nadendla GC-MS url:http://purl.bioontology.org/ontology/MESH/D008401 https://github.com/obi-ontology/obi/issues/1417 CFDE gas chromatography mass spectrometry assay An analyte assay that uses aptamers to detect protein analytes in serum. Bjoern Peters Randi Vita Rohloff JC, et al. Nucleic acid ligands with protein-like side chains: modified aptamers and their uses as diagnostic and therapeutic agents. Mol Ther Nucleic Acids. 2014;3:e201. https://github.com/obi-ontology/obi/issues/1308 ImmPort SOMAscan assay A proximity extension assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of proteins using a high-multiplex, high-throughput protein biomarker platform. The assay utilizes two distinct oligonucleotide-labeled antibodies (‘probes’) that bind at different sites for each detected protein. When the two probes are in close proximity, a new PCR target sequence is formed by a proximity-dependent DNA polymerization event. The resulting sequence is subsequently detected and quantified using standard real-time PCR. Bjoern Peters Hector Guzman-Orozco Randi Vita https://www.olink.com/ https://github.com/obi-ontology/obi/issues/1308 ImmPort Olink assay An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex. Bjoern Peters Hector Guzman-Orozco Randi Vita Bjoern Peters https://github.com/obi-ontology/obi/issues/1308 ImmPort proximity extension assay Illumina MiniSeq Whole genome sequencing of Klebsiella pneumoniae ST11 was performed using an Illumina Miniseq Sequencing System. PMID:31493526 A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. PERSON: Bonita Lam MiniSeq url:https://www.illumina.com/systems/sequencing-platforms/miniseq.html Illumina MiniSeq A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest. CMI-PB CMI-PB https://github.com/obi-ontology/obi/issues/1399 antigen detection by cytometric bead array assay A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest. CMI-PB CMI-PB https://github.com/obi-ontology/obi/issues/1399 antibody detection by cytometric bead array assay An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex. Bjoern Peters Hector Guzman-Orozco IEDB https://github.com/obi-ontology/obi/issues/1380 3D molecular structure determination assay A 3D molecular structure determination assay that uses electron microscopy imaging. Bjoern Peters Hector Guzman-Orozco IEDB https://github.com/obi-ontology/obi/issues/1380 electron-microscopy 3D molecular structure determination assay A complex of molecular entitites which is the result of an antibody binding to an antigen. Bjoern Peters Hector Guzman-Orozco IEDB antigen:antibody complex A complex of molecular entities which is the result of a T cell receptor binding to a MHC-epitope complex. Bjorne Peters Hector Guzman-Orozco IEDB epitope:MHC:TCR complex A complex of molecular entities which is the result of a MHC molecule binding with a ligand. Bjorne Peters Hector Guzman-Orozco IEDB MHC:ligand complex A 3D structure determination assay that determines the 3-dimensional configuration of a cell. Hector Guzman-Orozco Patrick Ray Hector Guzman-Orozco Patrick Ray https://github.com/obi-ontology/obi/issues/1364 3D cell structure determination assay A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell. Hector Guzman-Orozco Patrick Ray Hector Guzman-Orozco Patrick Ray https://github.com/obi-ontology/obi/issues/1364 Allen Institute for Brain Science 3D neural cell structure determination assay A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron. Hector Guzman-Orozco Patrick Ray Patrick Ray https://github.com/obi-ontology/obi/issues/1364 Allen Institute for Brain Science neuron morphology assay A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons. Patrick Ray MORF genetic sparse labeling https://biccn.org/teams/u01-yang https://doi.org/10.1016/j.neuron.2020.07.019 https://github.com/obi-ontology/obi/issues/1364 Allen Institute for Brain Science mosaicism with repeat frameshift genetic sparse labeling A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST). The representation of the morphology (3D structure) of a neuron can be a summary of various measurements relating to the dimensions of the neuron in question. Hector Guzman-Orozco Patrick Ray http://doi.org/10.1101/675280 https://github.com/obi-ontology/obi/issues/1364 Allen Institute for Brain Science neuron morphology reconstruction assay An immune epitope assay that characterizes the structrue of an antibody-epitope complex, or measures the binding of an antibody receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope. IEDB IEDB B cell assay|any method B cell epitope assay An immune epitope assay that characterizes the structrue of an epitope-T cell receptor complex, or measures the binding of a T cell receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope. IEDB IEDB T cell assay|any method T cell epitope assay 129/Sv male mice were injected with ENU and mated to C57BL/6 females. Their first-generation (G1) male progeny were again crossed to C57BL/6 females, and then backcrossed to one of their second-generation (G2) daughters to yield a third-generation (G3). PMID:18802465 A form of random mutagenesis that produces a mutation by introducing the organism to a chemical mutagen. Equivalent to FlyBase "chemical" (FBcv:0000525) in the origin of mutation branch and Dd mutagenesis meth0d term chemical mutagenesis (DDMUMET:0000014). Susan Bello ORCID:orcid.org/0000-0003-4606-0597 url:https://pubmed.ncbi.nlm.nih.gov/25646611/ chemical mutagenesis Groups of (101 x C3H)F1 hybrid male mice 11 weeks old were exposed to two different doses of 137Cs gamma rays. PMID:7035547 A form of random mutagenesis that produces a random mutation by exposing the organism to radiation. Equivalent to FlyBase "irradiation" (FBcv:0000503) in the origin of mutation branch. Susan Bello ORCID:orcid.org/0000-0003-4606-0597 radiation induced mutagenesis url:http://purl.obolibrary.org/obo/FBcv_0000503 irradiation mutagenesis Exons 20 and 21 were targeted for deletion because they encode the signature and Walker B motifs of the first ATP-binding domain, elements that are known to be critical for ABCA1 function. PMID:15550377 An induced mutation in which a specific gene(s) or part of a gene(s) is altered. Susan Bello ORCID:orcid.org/0000-0003-4606-0597 url:https://www.ncbi.nlm.nih.gov/books/NBK21878/def-item/A4754/ directed mutagenesis We have generated a WMS mouse model with S236X mutation in ADAMTS10 which is similar to the R237X mutation identifiedin WMS patients using CRISPR-Cas9. PMID:30060141 A directed mutagenesis in which guide RNAs and an endonuclease (cas9, TALEN) are used to introduce a mutation at a specific location in a gene. Equivalent to FlyBase term "site specific cleavage" (FBcv:0003007) in the origin of mutation branch. Susan Bello ORCID:orcid.org/0000-0003-4606-0597 url:https://pubmed.ncbi.nlm.nih.gov/28177771/ endonuclease mediated mutagenesis Briefly, to create Adar1 M249A/M249A mice, guide RNA targeting 5’-ACCTTCTGAGCCTCTTGACA-3’ was synthesized by using Gene Art Precisiong RNA Synthesis Kit (ThermoFisherScientific). Pronuclear-stage mouse embryos (CLEA Japan Inc., Tokyo, Japan) were electroporated to introduce Cas9 mRNA, the guide RNA and a single-stranded donor... PMID:33983932 An endonuclease mediated mutagenesis in which guide RNAs and cas are used to introduce a mutation at a specific location in the genome. Equivalent (narrow match) to FlyBase term "CRISPR/Cas9" (FBcv:0003008, narrow match as the OBI term covers all forms of cas) in the origin of mutation branch and Dd mutagenesis method term "CRISPR/Cas9" (DDMUMET:0000025). Susan Bello ORCID:orcid.org/0000-0003-4606-0597 CRISPR mediated mutagenesis CRISPR/cas mediated mutagenesis url:https://pubmed.ncbi.nlm.nih.gov/28177771/ cas mediated mutagenesis We designed transcription activator-like effector nucleases (TALENs) and a single-stranded oligo (ssOligo) donor template to edit the endogenous Actb locus within the mouse genome. PMID:30012594 An endonuclease mediated mutagenesis in which guide RNAs and transcription activator-like effector nucleases (TALENs) are used to introduce a mutation at a specific location in the genome. Equivalent to FlyBase term "TALEN" (FBcv:0003009) in the origin of mutation branch. Susan Bello ORCID:orcid.org/0000-0003-4606-0597 url:https://pubmed.ncbi.nlm.nih.gov/23664777/ TALEN mediated mutagenesis ZFN constructs targeting the third exon of the mouse Apoc2 gene were designed and synthetized by Sigma Aldrich... PMID:26574515 An endonuclease mediated mutagenesis in which synthetic zinc-finger proteins designed to target specific DNA sequences are used to introduce a mutation at a specific location in the genome. Equivalent to FlyBase term "ZFN" (FBcv:0003239) in the origin of mutation branch. Susan Bello ORCID:orcid.org/0000-0003-4606-0597 ZFN mediated mutagenesis url:https://pubmed.ncbi.nlm.nih.gov/23664777/ zinc finger mediated mutagenesis Transgenic mice were then generated by pronuclear injection of either the mixed MoPrP-PS1 and MoPrP-APP or the bicistronic MoPrP–APP/IRES/PS1 expression cassettes into single cell embryos derived from F2 hybrids of C57BL/6J and C3H/HeJ mice... PMID:11337275 A form of random mutagenesis that produces a mutation by introducing a construct into the genome of an organism in a random or semi-random fashion. Susan Bello ORCID:orcid.org/0000-0003-4606-0597 url:https://pubmed.ncbi.nlm.nih.gov/23996268/ transgenic mutagenesis Constructs lacking a promoter and including a B3-galactosidase gene, or a reporter gene encoding a protein with both B3-galactosidase and neomycin phosphotransferase activity, were designed so that activation of the reporter gene depends on its insertion within an active transcription unit. PMID:1653172 A transgenic mutagenesis that produces a mutation by introducing a construct designed to capture the expression of an endogenous gene by creating a spliced fusion transcript when inserted into the genome of an organism. Susan Bello ORCID:orcid.org/0000-0003-4606-0597 url:https://pubmed.ncbi.nlm.nih.gov/17877761/ gene-trap mutagenesis We generated several lines of enhancer trap mice carrying an enhancer detector cassette expressing Cre recombinase under the transcriptional control of the minimal promoter (129 base pairs) of the mouse Thy-1.2 gene. PMID:22492032 A transgenic mutagenesis that produces a mutation by introducing a construct designed to monitor transcriptionally active regions when inserted into the genome of an organism by inserting a reporter gene that requires cis-acting DNA sequences in the genome to activate reporter gene expression. Susan Bello ORCID:orcid.org/0000-0003-4606-0597 url:https://pubmed.ncbi.nlm.nih.gov/17877761/ enhancer-trap mutagenesis To disrupt the mdr1a gene a 1.6 kb NheI genomic fragment containing exons 6 and 7 was replaced by a hygromycin phosphotransferase cassette in a targeting vector. PMID:7910522 A directed mutation in which a construct is used to introduce a mutation into a specific genome location through homologous recombination. Equivalent to FlyBase term "gene targeting by homologous recombination" (FBcv:0000710) in the origin of mutation branch. Susan Bello ORCID:orcid.org/0000-0003-4606-0597 gene targeting by homologous recombination url:https://pubmed.ncbi.nlm.nih.gov/23996268/ targeted mutagenesis In order to achieve SB transposon-mediated mutagenesis in mice, we employed the gene trap scheme using a novel transposon vector, and we have generated a large number of mutant mice, approximately 30% of which displayed the phenotype. PMID:16880528 A random mutagenesis in which expression of a transposase causes the mobilization of an artificial or modified transposable element with the insertion of the element into the genome creating a mutation. Equivalent to FlyBase "transposable element activity" (FBcv:0000483) in the origin of mutation branch. Susan Bello ORCID:orcid.org/0000-0003-4606-0597 url:https://pubmed.ncbi.nlm.nih.gov/32050713/ transposon-induced mutagenesis A binding datum that is expressed as a categorical value. IEDB qualitative binding datum IEDB categorical binding datum A binding datum that is expressed using numbers. IEDB IEDB quantitative binding datum A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50). Bjoern Peters Hector Guzman-Orozco IEDB EC50 binding datum A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50). Bjoern Peters Hector Guzman-Orozco IEDB IC50 binding datum An assay that detects the binding of a MHC molecule with a ligand, and produces a quantitative measurement of the binding as an output. IEDB IEDB quantitative binding|binding assay assay measuring quantitative binding of a MHC:ligand complex An assay that detects the binding of an antigen with an antibody, and produces a quantitative measurement of the binding as an output. IEDB IEDB quantitative binding|binding assay assay measuring quantitative binding of an antigen:antibody complex An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a quantitative measurement of the binding as an output. IEDB IEDB quantitative binding|binding assay assay measuring quantitative binding of an epitope:MHC:TCR complex An albumin assay that measures the concentration of albumin in a specimen. James A. Overton albumin concentration assay A basophil assay that measures the percentage of basophils in a specimen. James A. Overton basophil percentage assay A calcium cation assay that measures the concentration of calcium cations in a specimen. James A. Overton calcium cation concentration assay A chloride assay that measures the concentration of chloride in a specimen. James A. Overton chloride concentration assay A cholesterol assay that measures the concentration of cholesterol in a specimen. James A. Overton cholesterol concentration assay A creatinine assay that measures the concentration of creatinine in a specimen. James A. Overton creatinine concentration assay An eosinophil assay that measures the percentage of eosinophils in a specimen. James A. Overton eosinophil percentage assay A globulin assay that measures the concentration of globulin in a specimen. James A. Overton globulin concentration assay A hemoglobin assay that measures the amount of hemoglobin in a specimen. James A. Overton hemoglobin concentration assay A high-density lipoprotein cholesterol assay that measures the concentration of high-density lipoprotein cholesterol in a specimen. James A. Overton high-density lipoprotein cholesterol concentration assay An iron assay that measures the concentration of iron cation in a specimen. James A. Overton iron concentration assay A low-density lipoprotein cholesterol assay that measures the concentration of low-density lipoprotein cholesterol in a specimen. James A. Overton low-density lipoprotein cholesterol concentration assay A lymphocyte assay that measures the percentage of lymphocytes in a specimen. James A. Overton lymphocyte percentage assay A metamyelocyte assay that measures the number of metamyelocytes in a specimen. James A. Overton metamyelocyte count assay A metamyelocyte assay that measures the percentage of metamyelocytes in a specimen. James A. Overton metamyelocyte percentage assay A methemoglobin assay that measures the percentage of methemoglobin in a specimen. James A. Overton methemoglobin percentage assay A monocyte assay that measures the percentage of monocytes in a specimen. James A. Overton monocyte percentage assay A myelocyte assay that measures the number of myelocytes in a specimen. James A. Overton myelocyte count assay A neutrophil assay that measures the percentage of neutrophils in a specimen. James A. Overton neutrophil percentage assay A phosphate ion assay that measures the concentration of phosphate ions in a specimen. James A. Overton phosphate ion concentration assay A potassium(1+) assay that measures the concentration of potassium(1+) in a specimen. James A. Overton potassium(1+) concentration assay A reticulocyte assay that measures the percentage of reticulocytes in a specimen. James A. Overton reticulocyte percentage assay A sodium(1+) assay that measures the concentration of sodium(1+) in a specimen. James A. Overton sodium(1+) concentration assay A thyroid stimulating hormone assay that measures the concentration of thyroid stimulating hormone in a specimen. James A. Overton thyroid stimulating hormone concentration assay A triglyceride assay that measures the concentration of triglycerides in a specimen. James A. Overton triglyceride concentration assay A 3,3',5'-triiodothyronine assay that measures the concentration of 3,3',5'-triiodothyronine in a specimen. James A. Overton 3,3',5'-triiodothyronine concentration assay A fibrinogen assay that measures the concentration of fibrinogen in a specimen. James A. Overton fibrinogen concentration assay A thyroxine assay that measures the concentration of free thyroxine in a specimen. James A. Overton free thyroxine concentration assay A thyroxine assay that measures the concentration of total thyroxine in a specimen. James A. Overton total thyroxine concentration assay A bilirubin IXalpha assay that measures the concentration of direct bilirubin in a specimen. James A. Overton direct bilirubin concentration assay A bilirubin IXalpha assay that measures the concentration of indirect bilirubin in a specimen. James A. Overton indirect bilirubin concentration assay A bilirubin IXalpha assay that measures the concentration of total bilirubin in a specimen. James A. Overton total bilirubin concentration assay A hemoglobin assay that measures the average concentration of hemoglobin in a population of erythrocytes. James A. Overton mean cell hemoglobin assay A hemoglobin assay that measures the concentration of hemoglobin in a specimen. James A. Overton mean cell hemoglobin concentration assay A platelet assay that measures the average volume of platelets in a specimen. James A. Overton mean platelet volume assay A neutrophil assay that measures the number of immature neutrophils in a specimen. James A. Overton immature neutrophil count assay An neutrophil assay that measures the percentage of immature neutrophils in a specimen. James A. Overton immature neutrophil percentage assay An erythrocyte assay that measures the percentage of nucleated erythrocytes in a specimen. James A. Overton nucleated erythrocyte percentage assay An erythrocyte assay that measures the average volume of erythrocytes in a specimen. James A. Overton mean cell volume assay A cytometry assay that measures the abundance and/or characteristics of erythrocytes. James A. Overton erythrocyte assay A hematocrit assay that measures the percentage of erythrocytes in a specimen by manual processes. James A. Overton manual hematocrit assay An analyte assay that measures the abundance of adiponectin James A. Overton adiponectin assay An adiponectin assay that measures the concentration of adiponectin in a specimen. James A. Overton adiponectin concentration assay An analyte assay that measures the abundance of creatine James A. Overton creatine assay A creatine assay that measures the concentration of creatine in a specimen. James A. Overton creatine concentration assay An analyte assay that measures the abundance of estradiol James A. Overton estradiol assay An estradiol assay that measures the concentration of estradiol in a specimen. James A. Overton estradiol concentration assay An analyte assay that measures the abundance of leptin James A. Overton leptin assay An leptin assay that measures the concentration of leptin in a specimen. James A. Overton leptin concentration assay An analyte assay that measures the abundance of lipoprotein James A. Overton lipoprotein concentration assay A lipoprotein concentration assay that measures the concentration of high-density lipoprotein in a specimen. James A. Overton high-density lipoprotein concentration assay A lipoprotein concentration assay that measures the concentration of low-density lipoprotein in a specimen. James A. Overton low-density lipoprotein concentration assay A lipoprotein concentration assay that measures the concentration of very-low-density lipoprotein in a specimen. James A. Overton very-low-density lipoprotein concentration assay An analyte assay that measures the abundance of luteinizing hormone James A. Overton luteinizing hormone assay A luteinizing hormone assay that measures the concentration of luteinizing hormone in a specimen. James A. Overton luteinizing hormone concentration assay An analyte assay that measures the abundance of nitrite James A. Overton nitrite assay A nitrite assay that measures the concentration of nitrite in a specimen. James A. Overton nitrite concentration assay An analyte assay that measures the abundance of phospholipid James A. Overton phospholipid assay A phospholipid assay that measures the concentration of phospholipids in a specimen. James A. Overton phospholipid concentration assay An analyte assay that measures the abundance of progesterone James A. Overton progesterone assay A progesterone assay that measures the concentration of progesterone in a specimen. James A. Overton progesterone concentration assay An analyte assay that measures the abundance of testosterone James A. Overton testosterone assay A testosterone assay that measures the concentration of testosterone in a specimen. James A. Overton testosterone concentration assay An analyte assay that measures the abundance of bile salt James A. Overton bile salt assay A bile salt assay that measures the concentration of bile salt in a specimen. James A. Overton bile salt concentration assay An analyte assay that measures the abundance of fatty acid James A. Overton fatty acid assay A fatty acid assay that measures the concentration of free fatty acids in a specimen. James A. Overton free fatty acid concentration assay An analyte assay that measures the abundance of insulin James A. Overton insulin assay A insulin assay that measures the concentration of insulin in a specimen. James A. Overton insulin concentration assay An analyte assay that measures the abundance of follicle stimulating hormone James A. Overton follicle stimulating hormone assay A follicle stimulating hormone assay that measures the concentration of follicle stimulating hormone in a specimen. James A. Overton follicle stimulating hormone concentration assay A lymphocyte assay that measures the number of lymphocytes and large unstained cells in a specimen. James A. Overton total lymphocyte count assay A lymphocyte assay that measures the percentage of lymphocytes and large unstained cells in a specimen. James A. Overton total lymphocyte percentage assay A cytometry assay that detects the presence of cells that secrete a material of interest (analyte). In the assay, a plate is coated with an antibody specific to the analyte of interest. These antibodies capture the analytes secreted by the cells. The analytes are then detected using fluorescent labeled secondary antibodies. Hector Guzman-Orozco FLUOROSPOT https://en.wikipedia.org/wiki/ELISpot#Mechanism_of_FluoroSpot https://github.com/obi-ontology/obi/issues/1414 CMI-PB fluorescent immunospot assay A proteomics profiling assay that detects proteins in a blood plasma specimen. Hector Guzman-Orozco CMI-PB https://github.com/obi-ontology/obi/issues/1414 CMI-PB plasma proteomics assay A flow cytometry assay that detects the presence/amount of antigen-specific T cells without the need to identify their cytokine production. Instead, antigen-specific T cells are detected on the basis of upregulation of TCR stimulation-induced surface markers. Hector Guzman-Orozco https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4955771/ https://github.com/obi-ontology/obi/issues/1414 CMI-PB T cell activation induced marker assay A blood specimen collection in which white blood cells are separated from a blood specimen. Hector Guzman-Orozco https://en.wikipedia.org/wiki/Leukapheresis leukapheresis An assay that has a cerebrospinal fluid specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 cerebrospinal fluid assay An assay that has an endotracheal aspirate specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 endotracheal aspirate assay An assay that has an induced sputum specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 induced sputum assay An assay that has a lung specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 lung assay An assay that has a milk specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 milk assay An assay that has a feces specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 feces assay An assay that has an umbilical cord blood specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 umbilical cord blood assay An assay that has a saliva specimen as evaluant. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 saliva assay An organism detection assay that detects microorganisms in a cerebrospinal fluid specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 cerebrospinal fluid microbiology assay An organism detection assay that detects microorganisms in an endotracheal aspirate specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 endotracheal tube aspirate microbiology assay An organism detection assay that detects microorganisms in an induced sputum specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 induced sputum microbiology assay A data entity that is the specified output of a blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 blood assay datum An organism detection datum that is the specified output of a blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 blood microbiology datum A data entity that is the specified output of a feces assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 feces assay datum An organism detection datum that is the specified output of a feces microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 feces microbiology datum A data entity that is the specified output of a urine assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 urine assay datum An organism detection datum that is the specified output of a urine microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 urine microbiology datum A data entity that is the specified output of a induced sputum assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 induced sputum assay datum An organization that performs assays, processes specimens, analyses data and conducts planned processes relevant to the life sciences. Christian Stoeckert ORCID:0000-0002-5714-991X Jie Zheng ORCID:0000-0002-2999-0103 laboratory OBIB eagle-i resource ontology ERO_0000001 https://github.com/obi-ontology/obi/issues/1436 OBIB biomedical laboratory organization An organism detection datum that is the specified output of an induced sputum microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 induced sputum microbiology datum A data entity that is the specified output of a cerebrospinal fluid assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 cerebrospinal fluid assay datum An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 cerebrospinal fluid microbiology datum An organism detection datum that is the specified output of an endotracheal aspirate assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 endotracheal aspirate assay datum An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 endotracheal tube aspirate microbiology datum An organism detection datum that is the specified output of a lung microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 lung microbiology datum An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 nasopharyngeal or oropharyngeal swab microbiology datum An organism detection datum that is the specified output of a pleural fluid microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 pleural fluid microbiology datum A data entity that is the specified output of an umbilical cord blood assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 umbilical cord blood assay datum An organism detection datum that is the specified output of an umbilical cord blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 umbilical cord blood microbiology datum A blood microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in blood datum A blood microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in blood datum A blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in blood datum A feces microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in feces datum A feces microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in feces datum A feces microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in feces datum A urine microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in urine datum An induced sputum microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in induced sputum datum An induced sputum microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in induced sputum datum An induced sputum microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in induced sputum datum An endotracheal tube aspirate microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in endotracheal tube aspirate datum A lung microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in lung datum A lung microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in lung datum A lung microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in lung datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in nasopharyngeal or oropharyngeal swab datum A nasopharyngeal or oropharyngeal swab microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in nasopharyngeal or oropharyngeal swab datum A pleural fluid microbiology datum that is about bacteria. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 bacteria in pleural fluid datum A pleural fluid microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in pleural fluid datum A pleural fluid microbiology datum that is about a virus. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 virus in pleural fluid datum An umbilical cord blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1428 eukaryota in umbilical cord blood datum An organism detection assay that detects microorganisms in a lung specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 lung microbiology assay An organism detection assay that detects microorganisms in a pleural fluid specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 pleural fluid microbiology assay An organism detection assay that detects microorganisms in an umbilical cord blood specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 umbilical cord blood microbiology assay An organism detection assay that detects microorganisms in a nasopharyngeal or oropharyngeal swab specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 nasopharyngeal or oropharyngeal swab microbiology assay An organism detection assay that detects microorganisms in a urine specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1429 urine microbiology assay A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. John Judkins multiplexed real time polymerase chain reaction assay VEuPathDB https://github.com/obi-ontology/obi/issues/1431 multiplex real time polymerase chain reaction assay A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle. John Judkins multiplexed real time reverse-transcription polymerase chain reaction assay VEuPathDB https://github.com/obi-ontology/obi/issues/1431 multiplex real time reverse-transcription polymerase chain reaction assay A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1439 mosquito membrane feeding device Testing the effectiveness of drugs or antibodies against parasite transmission. An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1439 mosquito membrane feeding assay A study design that is executed primarily on a computer. Hector Guzman-Orozco https://en.wikipedia.org/wiki/In_silico https://github.com/obi-ontology/obi/issues/1430 CMI-PB in silico design A cytometric bead array assay that detects epitope specific granulysin release by T cells. IEDB IEDB granulysin release|cytometric bead array cytometric bead array assay measuring epitope specific granulysin release by T cells A cytometric bead array assay that detects epitope specific perforin release by T cells. IEDB IEDB perforin release|cytometric bead array cytometric bead array assay measuring epitope specific perforin release by T cells A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating. John Judkins NCIT:C85736 https://www.cdc.gov/dpdx/diagnosticprocedures/stool/staining.html https://github.com/obi-ontology/obi/issues/1444 modified acid-fast stain microscopy assay A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex. Bjoern Peters Hector Guzman-Orozco IEDB positive binding datum PMID: 11329444.Clin Diagn Lab Immunol. 2001 May. Development of a Novel In Vitro Assay (ALS Assay) for Evaluation of Vaccine-Induced Antibody Secretion from Circulating Mucosal Lymphocytes. An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells. John Judkins ALS assay antibodies from lymphocyte supernatant assay OBI VEuPathDB https://github.com/obi-ontology/obi/issues/1443 antibodies from lymphocyte secretions assay A DNA sequencing assay that uses tyramide signal amplification (TSA) to assess distance of DNA regions to a targeted nuclear compartment or protein, typically on a scale of 100-1000 nm. Michelle Giglio Suvarna Nadendla TSA-seq EFO:0009971 PMID:30154186 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN tyramide signal amplification sequencing assay An assay for identifying DNA binding sites for a protein by fusing it to Dam methylase, and expressing it so that bound DNA gets methylated. The methylated DNA can then be isolated and analyzed. Michelle Giglio Suvarna Nadendla DamID assay EFO:0008704 PMID:17545983 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN DNA adenine methyltransferase identification assay A DNA adenine methyltransferase identification (DamID) assay in which DamID-generated DNA fragments undergo high-throughput sequencing to determine a protein's DNA-binding site. Michelle Giglio Suvarna Nadendla 4DN DCIC https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN DamID-seq A DNA sequencing assay in which nucleoli are isolated and the DNA associated with them is sequenced to identify nucleoli-associating domains. Michelle Giglio Suvarna Nadendla NAD-seq EFO:0009972 PMID:31201210 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN nucleolus-associated domain sequencing assay A Hi-C assay in which DNase I is used for digesting DNA fragments rather than a restriction enzyme, which can result in a higher resolution of mapped chromosome contacts. Michelle Giglio Suvarna Nadendla EFO:0009976 PMID:27685100 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN DNase Hi-C assay A Hi-C assay which uses micrococcal nuclease digestion in place of the restriction enzyme digestion step. Michelle Giglio Suvarna Nadendla EFO:0008808 PMID:26119342 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN micro-C assay A Hi-C assay performed on massively multiplexed single-cell samples. Michelle Giglio Suvarna Nadendla sci-Hi-C EFO:0009977 PMID:28135255 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN single cell combinatorial indexing Hi-C assay A Hi-C assay performed on isolated nuclei. Michelle Giglio Suvarna Nadendla sn-Hi-C EFO:0009978 PMID:28355183 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN single nucleus Hi-C assay A Hi-C assay performed on a single cell. Michelle Giglio Suvarna Nadendla EFO:0009979 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN single cell Hi-C assay A Hi-C assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells. Michelle Giglio Suvarna Nadendla 4DN DCIC https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN bulk Hi-C assay A Hi-C assay that assesses interactions between multiple DNA fragments rather than only pairwise interactions as in traditional Hi-C. The experimental procedure of cross-linking, digestion, and ligation is performed similarly to traditional Hi-C, but after DNA is purified a long-read library is produced in which many ligated fragments may be contained in a single molecule. The library is then sequenced on a long read sequencer. Michelle Giglio Suvarna Nadendla MC-3C MC-HI-C The 4D Nucleome Network https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN multi-contact Hi-C assay A DNA sequencing assay designed to detect interacting genomic regions. Rather than the traditional Hi-C approach of digestion and proximity ligation, the procedure involves transposase-mediated insertion of an oligonucleotide linker between the pair of interacting regions. Michelle Giglio Suvarna Nadendla TrAC-Loop EFO:0009982 PMID:30150754 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN transposase-mediated analysis of chromatin looping assay A sequencing assay designed to detect multi-way interactions between nucleic acids. The procedure involves crosslinking nuclei, and then splitting the lysate among wells in a 96-well or other multi-well plate. A different barcode is ligated to the fragments in each well, and the lysates are pooled together again. This sequence of splitting, tagging, and re-combining is repeated several times so that fragments with the same sequences of barcodes represent fragments that have co-associated throughout the experiment. Finally, a sequencing library is constructed and high-throughput sequencing is performed. Michelle Giglio Suvarna Nadendla SPRITE EFO:0009984 PMID:29887377 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN split-pool recognition of interactions and tag extension assay A split-pool recognition of interactions and tag extension (SPRITE) assay that only assays interactions between regions of genomic DNA. Michelle Giglio Suvarna Nadendla DNA SPRITE EFO:0009985 PMID:29887377 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN DNA split-pool recognition of interactions and tag extension assay A split-pool recognition of interactions and tag extension (SPRITE) assay in which RNA in the cross-linked complexes is converted to cDNA before the initial splitting step, allowing analysis of RNA-DNA interactions. Michelle Giglio Suvarna Nadendla RNA-DNA SPRITE EFO:0009986 PMID:29887377 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN RNA-DNA split-pool recognition of interactions and tag extension assay A DNA sequencing assay designed to analyze 3D chromatin structure without relying on digestion and ligation. The procedure involves cryosectioning samples in random orientation, and then single nuclear profiles are isolated by laser microdissection. Each nuclear profile then undergoes high-throughput sequencing, and subsequent analysis can generate a matrix of inferred proximity between genomic regions. Michelle Giglio Suvarna Nadendla GAM EFO:0009987 PMID:28273065 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN genome architecture mapping assay A nuclear ligation assay for probing RNA-DNA interactions in the nucleus. Nuclei are crosslinked, and RNA fragments are ligated to proximal DNA fragments via a special linker molecule. After reverse transcription, high-throughput sequencing is performed. Michelle Giglio Suvarna Nadendla MARGI EFO:0009988 PMID:28132817 https://github.com/obi-ontology/obi/issues/1472 CFDE-4DN mapping RNA-genome interactions assay A T cell epitope specific cytokine production assay that detects amphiregulin production by T cells. IEDB IEDB amphiregulin release|biological activity assay measuring epitope specific amphiregulin production by T cells An enzyme-linked immunosorbent assay that detects amphiregulin production by T cells. IEDB IEDB amphiregulin release|ELISA ELISA measuring epitope specific amphiregulin production by T cells The release of perforin during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters perforin release during T cell degranulation The release of granzyme A during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters granzyme A release during T cell degranulation The release of granzyme B during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters granzyme B release during T cell degranulation The release of granulysin during cytotoxic T cell degranulation. Bjoern Peters Hector Guzman-Orozco Alexander Diehl, Bjoern Peters granulysin release during T cell degranulation A blood microbiology assay that detects a microorganism in a venous blood specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1491 venous blood microbiology assay Next-generation high-density peptide microarrays measuring antibody responses to overlapping peptides: PMID:25922409. A B cell epitope assay that measures the binding of an antibody receptor to an epitope using a high throughput multiplexed assay. IEDB IEDB antibody binding|High throughput multiplexed assay high throughput multiplexed assay measuring binding of a B cell epitope:antibody complex Adaptive Biotech multiplexed TCR sequencing assays: PMID:32793919. A T cell epitope assay that measures the binding of T cell receptor to an epitope using a high throughput multiplexed assay. IEDB IEDB T cell binding|High throughput multiplexed assay high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR complex Peptide microarray with fluorescence detection for millions of MHC binding measurements: PMID: 33705522. A MHC ligand assay that detects the binding of a ligand to an MHC molecule using a high throughput multiplexed assay. IEDB IEDB MHC binding|High throughput multiplexed assay high throughput multiplexed assay measuring binding of a MHC:ligand complex Mass spectrometry identified 35,367 and 28,132 HLA-class I ligands witth a false discovery rate: PMID: 29789417. A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them using a high throughput multiplexed assay. IEDB IEDB ligand presentation|High throughput multiplexed assay high throughput multiplexed assay measuring MHC ligand processing and presentation The output produced by a digital imaging technique, such as microscopy, MRI, or CT. A data set that is comprised of multidimensional structured measurements and metadata required for a morphological representation of an entity. An image data set can be the source from which an image (such as a 2D image using pixels or a 3D image using voxels) is produced. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 image data set The DICOM file produced by an MRI machine when a multiple sclerosis patient undergoes a brain scan. An image data set whose information content originates from some MR imaging assay and is about some MRI participant. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" MRI at a Glance, ISBN 10: 1119053552 https://github.com/obi-ontology/obi/issues/1481 magnetic resonance image data set The subject being scanned in an MRI study, and bearor of data derived from that study. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" magnetic resonance imaging participant An evaluant role that inheres in a material entity that is realized in a MR imaging assay in which MR imaging data is generated about the bearer of the evaluant role. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" magnetic resonance imaging evaluant role The untransformed ("k-space") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. An image data set that encodes measurement values produced by some instrument before undergoing a data transformation. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-1604-3078 "Alan Ruttenberg" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 raw image data set The NMR/MRI machine protocol about the radiofrequency pulse sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" magnetic resonance pulse sequence protocol The production of JPEG file by a digital camera. An image data set that is the output of an image data set analysis. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-1604-3078 "Alan Ruttenberg" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 computed image data set The product of a mathematical transformation of raw "k-space" data produced by an MRI machine into a form that represents the anatomical structure of the brain. An image data set that is the direct output of a raw magnetic resonance image data set reconstruction or a transformation of another MR image data set. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 reconstructed magnetic resonance image data set MRI used for assessing structural integrity of brain axons and visualizing ischemia. A type of magnetic resonance image data set collected using at least three diffusion gradients of some factor "b," which is a function of the amplitude, duration, and interval of the gradiants. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 diffusion weighted magnetic resonance image data set MRI used for assessing brain activity via blood oxygen level dependent signal. An magnetic resonance image data set collected as a 4D time series representing changes in brain metabolism (i.e. BOLD), typically used as a proxy for brain activity. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 functional magnetic resonance image data set An fMRI used for assessing functional connectivity of brain regions at rest. A type of functional MRI in which the participant is not given a task, but just rests during acquisision https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 resting state functional magnetic resonance image data set fMRI type used for assessing brain activity while performing an action or in response to stimuli. A type of functional MRI in which the participant is given a task or tasks, which are timed with the acquisition https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 task-based functional magnetic resonance image data set MRI used for evaluating ischemia. An magnetic resonance image data set that captures volume and flow of blood in the brain. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 perfusion weighted magnetic resonance image data set MRI used for visualizing structure of tissue. An magnetic resonance image data set in which the contrast emphasizes density of protons, supressing T1 and T2 effects https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 proton density magnetic resonance image data set MRI used for visualizing structure of tissue where fluid is hypointense. An magnetic resonance image acquired using a T1 weighted magnetic resonance image acquisition sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T1 weighted magnetic resonance image data set MRI used for assessing breakdown of blood brain barrier. A T1 weighted image data set where gadolidium contrast agent has been administered to the participant before image acquistion. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 post-Gd T1 weighted magnetic resonance image data set MRI used for computational research on the structure of tissue. T1 weighted image data set collected using a gradient recall echo sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T1 weighted GRE magnetic resonance image data set MRI used for computational segmentation of tissue due to high quality. A T1-weighted image data set acquired from an NMR/MRI machine with at least a 3 Tesla magnet and in which the voxel size is isotropic. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 high resolution T1 weighted magnetic resonance image data set First MRI acquired as part of longitudinal study. A T1w image data set collected at an evaluant's first visit in a study. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 baseline high resolution T1 weighted magnetic resonance image data set MRI acquired after the first scan as part of longitudinal study. A T1w image data set collected at a later time than the evaluant's first scan. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 follow-up high resolution T1 weighted magnetic resonance image data set MRI used for visualizing structure of tissue, often of lower quality than a GRE sequence. A T1 weighted image data set acquired using a spin echo sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T1 weighted SE magnetic resonance image data set MRI used for visualizing structure of tissue where fluid is hyperintense. A magnetic resonance image produced by a T2 weighted magnetic resonance image acquisition sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T2 weighted magnetic resonance image data set MRI used for visualizing lesions in multiple sclerosis. A T2 weighted image data set collected using a FLAIR sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T2 weighted FLAIR magnetic resonance image data set MRI used for visualizing structure of tissue with fast acquisition times. T2 weighted image collected using a fast/turbo spin echo sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" T2 weighted TSE magnetic resonance image data set https://github.com/obi-ontology/obi/issues/1481 T2 weighted FSE magnetic resonance image data set MRI used for visualizing structure of tissue, often longer acquisition than FSE sequence. A type of T2-weighted image in which the acquisition is performed using a 2D spin-echo technique https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T2 weighted SE magnetic resonance image data set MRI used for visualizing structure of tissue where signal from fat is suppressed. A T2 weighted magnetic resonance image data set collected using a STIR sequence to suppress the signal coming from fat. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 T2 weighted STIR magnetic resonance image data set MRI better suited for identifying focal pathology than T2w SE sequences. T2* weighted image data set collected using a gradient echo sequence. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://github.com/obi-ontology/obi/issues/1481 T2* weighted GRE magnetic resonance image data set The untransformed ("k-space") data produced by an MRI machine, prior to mathematical transformation into a form that corresponds to the anatomical structure of the brain. An image data set that is the direct output of an magnetic resonance imaging assay and whose values encode spatial frequencies produced by the NMR or MRI instrument. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 raw magnetic resonance image data set The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 image data set analysis A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined. A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 raw magnetic resonance image data set reconstruction The Desikan-Killiany brain region atlas used by the FreeSurfer software suite. An image data set consisting of values computed from multiple image data sets encoded to represent the spatial location of individual functional or structural regions of a canonical brain. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 brain region atlas image data set A brain atlas of resting-state functional networks derived from the probability that disparate brains regions are active at the same time. A brain atlas consisting of weighted values that respresent the probability that a voxel X is part of some brain component Y, typically derived from multiple image data sets. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 probabilistic brain region atlas image dataset The JHU white-matter tractography atlas used for mapping brain connectomes. A brain atlas consisting of discrete integer values where a value X denotes a voxel is part of some brain component Y. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 deterministic brain region atlas image data set The output of an algorithm that identifies pedestrians walking in a street from an image data set, where the output contains values only in the segment where the pedestrian is present. An image data set of integer values in which each value corresponds to some shared characteristic or computed property. The values often belong to a group of pixels or voxels that share the same characteristic, such as a tissue type or anatomical region. https://orcid.org/0000-0001-9625-1899 "William D. Duncan" https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie" https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith" https://github.com/obi-ontology/obi/issues/1481 image segmentation map The output produced by a manual or automated segmentation of lesions from a brain MRI. An image data set where voxel intensity values greater than zero encode the location of some brain lesion and voxels outside the lesion have an intensity value of zero. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 lesion mask The output produced by a manual or automated segmentation of lesions from a T1w MRI. A lesion mask where the lesions are derived from a T1 weighted image data set. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 T1 lesion mask The output produced by a manual or automated segmentation of lesions from a T2w FLAIR MRI. A lesion mask where the lesions are derived from a T2 FLAIR image data set. https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik" https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl" https://github.com/obi-ontology/obi/issues/1481 T2 FLAIR lesion mask A data entity that is the specified output of a milk assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1515 milk assay datum A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has or had a disease, disorder, or syndrome of a certain type, or none of these as output. Jie Zheng https://github.com/obi-ontology/obi/issues/1505 organism diagnostic process A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these. Jie Zheng https://github.com/obi-ontology/obi/issues/1505 diagnosis of an organism Using a radioactivity detection assay as part of a tritiated thymidine incorporation assay to determine the degree to which cells are replicating by detecting radioactivity of tritiated thymidine, where radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating. An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B. Bjoern Peters Hector Guzman-Orozco OBI https://github.com/obi-ontology/obi/issues/1488 detection technique assay kit Glutathione S-Transferase (GST) Assay Kit: https://www.sigmaaldrich.com/deepweb/assets/sigmaaldrich/product/documents/101/301/cs0410bul.pdf A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit. John Judkins OBI, VEuPathDB https://github.com/obi-ontology/obi/issues/1456 VEuPathDB assay kit A biological process where T cells produce XCL1 resulting from the recognition of a T cell epitope. IEDB IEDB epitope specific XCL1 release by T cells A T cell epitope specific cytokine production assay that detects lymphotactin production by T cells. IEDB IEDB lymphotactin release|biological activity assay measuring epitope specific lymphotactin production by T cells An enzyme-linked immunosorbent assay that detects lymphotactin production by T cells. IEDB IEDB lymphotactin release|ELISA ELISA measuring epitope specific lymphotactin production by T cells A telephone or video remote patient assessment conducted between a physician and patient. An organism diagnostic process which involves a remote assessment of a patient by a clinician. telehealth patient assessment 2022-05-02T14:15:39Z remote patient assessment An assay that combines electrophysiological, transcriptomic, and morphological characterization of individual neurons. In this approach, patch-clamp is used to generate an electrophysiological recording of the neuron, then the neuron's cytoplasm and/or nucleus is collected and processed for RNAseq, and finally the cell is simultaneously filled with a dye that allows for subsequent morphological reconstruction. Michelle Giglio Patrick Lloyd Ray Sebastian Duesing https://en.wikipedia.org/wiki/Patch-sequencing https://github.com/obi-ontology/obi/issues/1457 Patrick Lloyd Ray patch-seq assay A single-cell transcription profiling by RNA sequencing assay that analyzes mRNA transcripts from droplets of individual cells. The process involves the following steps: (1) prepare a single-cell suspension from a tissue; (2) co-encapsulate each cell with a distinctly barcoded microparticle (bead) in a nanoliter-scale droplet; (3) lyse cells after they have been isolated in droplets; (4) capture a cell’s mRNAs on its companion microparticle, forming STAMPs (single-cell transcriptomes attached to microparticles); (5) reverse-transcribe, amplify, and sequence. Michelle Giglio Patrick Lloyd Ray Sebastian Duesing Drop-seq Dropseq dropseq https://doi.org/10.1016/j.cell.2015.05.002 https://github.com/obi-ontology/obi/issues/1457 Patrick Lloyd Ray droplet-based single-cell RNA sequencing assay An assay that uses combinatorial indexing to generate a library of cDNA and open chromatin gDNA fragments by tagmenting a single nuclei and open chromatin, and encapsulating those in a droplet including both an oligo-dT-containing barcoded bead and a splint oligonucleotide, which links the tagmented gDNA fragments to the bead which capture both mRNAs and open chromatin fragments. Michelle Giglio Patrick Lloyd Ray Sebastian Duesing SNARE-seq2 https://doi.org/10.1038/s12276-020-0420-2 https://github.com/obi-ontology/obi/issues/1457 Patrick Lloyd Ray single-nucleus chromatin accessibility and mRNA expression sequencing 2 assay A single cell transcription profiling by RNA sequencing assay wherein cells are lysed and their recovered RNA is hybridized to an oligo(dT) that primes a reverse transcription reaction, the outcome of which are cDNA’s that have PCR handles on both ends. The cDNA's are then amplified using PCR, and the products are sequenced. Michelle Giglio Patrick Lloyd Ray Sebastian Duesing SMARTseq http://www.enseqlopedia.com/wiki-entry/rna-sequencing-methods/low-level-rna-detection/smart-seq/ https://github.com/obi-ontology/obi/issues/1457 Patrick Lloyd Ray switching mechanism at the 5' end of RNA template sequencing assay A single cell transcription profiling by RNA sequencing assay that is a variation on the switching mechanism at the 5' end of RNA template sequencing assay (SMARTseq) that allows the generation of full-length cDNA and sequencing libraries by using standard reagents. Michelle Giglio Patrick Lloyd Ray Sebastian Duesing SMARTseq2 https://doi.org/10.1038/nprot.2014.006 https://github.com/obi-ontology/obi/issues/1457 Patrick Lloyd Ray switching mechanism at the 5' end of RNA template sequencing 2 assay A specimen that is derived from placental blood. John Judkins VEuPathDB placental blood specimen A blood microbiology assay that detects microorganisms in a placental blood specimen. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 placental blood microbiology assay An organism detection datum that is the specified output of a placental blood microbiology assay. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 placental blood microbiology datum A placental blood microbiology datum that is about eukaryota. John Judkins VEuPathDB https://github.com/obi-ontology/obi/issues/1297 eukaryota in placental blood datum synaptosome preparation process A material component separation process where a synaptic terminal is isolated from a neuron by mild homogenization of nervous tissue under isotonic conditions and subsequent fractionation using differential and density gradient centrifugation. Michelle Giglio Suvarna Nadendla url:https://en.wikipedia.org/wiki/Synaptosome CFDE-GlyGen synaptosome preparation process Illumina HiSeq 1500 A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. Jain Aluvathingal Michelle Giglio Suvarna Nadendla HiSeq 1500 https://jp.support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/hiseq1500/hiseq-1500-system-guide-15035788-03.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Illumina HiSeq 1500 NextSeq 550 A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://www.illumina.com/systems/sequencing-platforms/nextseq.html https://github.com/obi-ontology/obi/issues/1546 gEAR Illumina NextSeq 550 Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 A DNA microarray manufactured with Agilent 60-mer SurePrint Technology .The SurePrint G3 Mouse Gene Expression 4x44K v2 Microarray provide full coverage of the mouse transcriptome using the latest annotation databases, including long non-coding RNA(lncRNA). Each glass slide is formatted with four high-definition 44K arrays. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://www.agilent.com/cs/library/brochures/IBS-231%20genomics%20catalog%20mech%20FINAL.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray A DNA microarray manufactured with Agilent 60-mer SurePrint Technology for studying exon-level gene expression changes. The SurePrint G3 Mouse Exon 4x180K Microarray include probes targeting individual exons. Each glass slide formatted with four 180K arrays. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://www.agilent.com/cs/library/brochures/5990-6928en_lo.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray A DNA microarray manufactured with Agilent 60-mer SurePrint technology which provides comprehensive coverage of genes and transcripts using the latest annotation databases. The SurePrint G3 Mouse Gene Expression 8x60K v2 Microarray features complete coverage of established RefSeq coding transcripts (NM) from the latest build and updated long non-coding RNA (lncRNA) content to ensure relevant research.Each glass slide formatted with eight high-definition 60K arrays. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://www.agilent.com/cs/library/usermanuals/public/G4140-90050_GeneExpression_TwoColor_6.9.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray Affymetrix Mouse Genome 430 2.0 Array A DNA microarray manufactured by Affymetrix, which includes complete coverage of the GeneChip Mouse Expression Set 430, for analysis of over 39,000 transcripts and variants from more than 34,000 well-characterized mouse genes and UniGene clusters, on a single array. The sequences for this array were selected from GenBank™, dbEST, and RefSeq., and sequence clusters cretaed from the UniGene database. Jain Aluvathingal Michelle Giglio Suvarna Nadendla GeneChip Mouse Genome 430 2.0 Array https://www.thermofisher.com/order/catalog/product/900497 https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Mouse Genome 430 2.0 Array Affymetrix Mouse Genome 430A 2.0 Array A DNA microarray manufactured by Affymetrix for gene expression analysis focusing on approximately 14,000 well-characterized genes in the transcribed mouse genome using single-array cartridge. Sequences used in the design of the array were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database. Jain Aluvathingal Michelle Giglio Suvarna Nadendla GeneChip Mouse Genome 430A 2.0 Array https://www.thermofisher.com/order/catalog/product/900500TS?SID=srch-srp-900500TS https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Mouse Genome 430A 2.0 Array Affymetrix Mouse Gene 1.0 ST Array A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). This whole-transcript array design provides a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile. Jain Aluvathingal Michelle Giglio Suvarna Nadendla GeneChip Mouse Gene 1.0 ST Array https://www.thermofisher.com/order/catalog/product/901168 https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Mouse Gene 1.0 ST Array Affymetrix Mouse Gene 2.1 ST Array A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA).To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db. Jain Aluvathingal Michelle Giglio Suvarna Nadendla GeneChip Mouse Gene 2.1 ST Array https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fbrochures%2Fmouse_gene_array_datasheet.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Mouse Gene 2.1 ST Array Affymetrix Rhesus Macaque Genome Array A DNA microarray manufactured by Affymetrix,which is a single-labeled high-density oligonucleotide array, designed to study gene expression in the rhesus animal model and to interrogate rhesus transcripts orthologous to the 3' end of human transcripts. The array consists of over 52,000 probe sets representing more than 20,000 genes, and several relevant viral organisms for studying host-disease immune response. Jain Aluvathingal Michelle Giglio Suvarna Nadendla GeneChip Rhesus Macaque Genome Array https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FMAN0017705_702023_RhesusArray_PI.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Rhesus Macaque Genome Array Affymetrix Human Transcriptome Array 2.0 A DNA microarray manufactured by Affymetrix, to go beyond gene-level expression profiling to accurately detect all known transcript isoforms produced by a gene. The array design covers >245,000 coding transcripts, >40,000 non-coding transcripts and >339,000 probe sets covering exon-exon junctions, thus ensuring uniform coverage of the transcriptome. Jain Aluvathingal Michelle Giglio Suvarna Nadendla GeneChip Human Transcriptome Array 2.0 https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fbrochures%2Fhta_array_2_0_datasheet.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Human Transcriptome Array 2.0 Affymetrix Human Genome U219 Array A DNA microarray manufactured by Affymetrix, which comprises more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation. Sequences used in the design of the array were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™. Jain Aluvathingal Michelle Giglio Suvarna Nadendla Applied Biosystems GeneChip PrimeView Human Gene Expression Array https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fmanuals%2FMAN0017681_703036_GeneChipPrimeViewArray_PI.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Human Genome U219 Array Affymetrix Human Gene 2.0 ST Array A DNA microarray manufactured by Affymetrix, which provides the most accurate, sensitive, and comprehensive measurement of protein coding (mRNA) and long intergenic non-coding RNA (lincRNA) transcripts. The array design covers >33,500 coding transcripts and >11,000 lincRNA transcripts thus enabling researchers to understand whole-transcriptome gene expression at the gene and exon levels, which allows the study of transcript variants and alternative splicing events. Jain Aluvathingal Michelle Giglio Suvarna Nadendla GeneChip Human Gene 2.0 ST Array https://www.thermofisher.com/document-connect/document-connect.html?url=https%3A%2F%2Fassets.thermofisher.com%2FTFS-Assets%2FLSG%2Fbrochures%2Fhugene_2_st_datasheet.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Human Gene 2.0 ST Array Affymetrix Clariom S Assay, Human A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the human transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers , and to quickly assess changes in key genes and pathways. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://www.thermofisher.com/order/catalog/product/902926#1_1 https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Clariom S Assay, Human Affymetrix Clariom S Assay, Mouse A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the mouse transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers, and to quickly assess changes in key genes and pathways. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://www.thermofisher.com/order/catalog/product/902931?SID=srch-srp-902931, https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Clariom S Assay, Mouse Illumina HumanHT-12 V4.0 expression beadchip An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling and expression-based quantitative trait loci (eQTL) studies. This BeadChip contains 12 arrays, each featuring more than 48,000 probes, targeting more than 31,000 annotated genes, providing genome-wide coverage of well-characterized genes, gene candidates, and splice variants. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://www.illumina.com/documents/products/technotes/technote_humanht_12_imputation.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Illumina HumanHT-12 V4.0 expression beadchip Illumina MouseRef-8 v2.0 beadchip An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling in the mouse.This Beadchip contains 8 microarrays, featuring more than 25,000 probes per array, derived from the NCBI RefSeq database and supplemented with MEEBO and RIKEN FANTOM2 content. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/arraykits/whole-genome-gene-expression/WGGEX_Direct_Hybridization_Assay_Guide_11322355_A.pdf, https://www.illumina.com/documents/products/datasheets/datasheet_gene_exp_analysis.pdf https://github.com/obi-ontology/obi/issues/1546 gEAR Illumina MouseRef-8 v2.0 beadchip Affymetrix Mouse Exon Junction Array A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the mouse transcriptome. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://academic.oup.com/bioinformatics/article/26/2/268/209989 https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Mouse Exon Junction Array Affymetrix Human Exon Junction Array A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the human transcriptome. Jain Aluvathingal Michelle Giglio Suvarna Nadendla https://academic.oup.com/bioinformatics/article/26/2/268/209989 https://github.com/obi-ontology/obi/issues/1546 gEAR Affymetrix Human Exon Junction Array linked-read sequencing assay A DNA sequencing assay that uses microfluidics to partition and barcode high molecular weight DNA such that short reads derived from fragments of the large piece of DNA can be assembled within the context of the high molecular weight piece of DNA they are derived from, facilitating the use of short read data to sequence and assemble large genomes. Michelle Giglio Sebastian Duesing Michelle Giglio https://github.com/obi-ontology/obi/issues/1559 CFDE linked-read sequencing assay An administration of substance in vivo with the intention to induce disease in the organism. IEDB IEDB administering substance in vivo to cause disease An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism. IEDB IEDB administering substance in vivo to reduce or prevent disease A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system. Chris Stoeckert Jie Zheng PBMC specimen http://en.wikipedia.org/wiki/Peripheral_blood_mononuclear_cell peripheral blood mononuclear cell specimen A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm. The Mother and Child Health and Education Trust mid-upper arm circumference datum A data entity that is the specified output of an antigen specific antibodies assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 antigen specific antibodies assay datum An antigen specific antibodies assay that has a blood specimen as evaluant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 VEuPathDB antigen specific antibodies in blood assay An antigen specific antibodies assay that has a milk specimen as evaluant. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 VEuPathDB antigen specific antibodies in milk assay An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 antigen specific antibodies in blood assay datum An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1526 antigen specific antibodies in milk assay datum An assay in which the level of catalytic activity of an enzyme is determined. James A. Overton enzymatic activity level assay An enzymatic activity level assay that measures the activity of 5'-nucleotidase in a sample. James A. Overton 5'-nucleotidase activity level assay An enzymatic activity level assay that measures the activity of alanine aminotransferase in a sample. James A. Overton alanine aminotransferase activity level assay An enzymatic activity level assay that measures the activity of alkaline phosphatase in a sample. James A. Overton alkaline phosphatase activity level assay An enzymatic activity level assay that measures the activity of amylase in a sample. James A. Overton amylase activity level assay An enzymatic activity level assay that measures the activity of aspartate aminotransferase in a sample. James A. Overton aspartate aminotransferase activity level assay An enzymatic activity level assay that measures the activity of cholinesterase in a sample. James A. Overton cholinesterase activity level assay An enzymatic activity level assay that measures the activity of creatine kinase in a sample. James A. Overton creatine kinase activity level assay An enzymatic activity level assay that measures the activity of gamma-glutamyltransferase in a sample. James A. Overton gamma-glutamyltransferase activity level assay An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample. James A. Overton glutamate dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample. James A. Overton isocitrate dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample. James A. Overton lactate dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample. James A. Overton sorbitol dehydrogenase activity level assay An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample. James A. Overton acyl-CoA oxidase activity level assay An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample. James A. Overton N-acetyl-beta-glucosaminidase activity level assay An enzymatic activity level assay that measures the activity of ribonuclease in a sample. James A. Overton ribonuclease activity level assay An enzymatic activity level assay that measures the activity of galactosidase in a sample. James A. Overton galactosidase activity level assay An arthropod trap that is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. This trap has the same design as the Mosquito Magnet Pro trap but is smaller, is more lightweight, and uses a main line electricity supply instead of propane to power itself. Both use propane to produce the arthropod attractor. VEuPathDB https://github.com/obi-ontology/obi/issues/1523 Mosquito Magnet Liberty Plus trap The administration of a malignant cell to a host. Hector Guzman-Orozco IEDB tumor challenge in vivo challenge The administration of a challenge to a live host. Hector Guzman-Orozco IEDB in vivo challenge An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. Hector Guzman-Orozco survival after infectious challenge IEDB https://github.com/obi-ontology/obi/issues/1594 epitope protection from infectious challenge experiment based on survival An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls. Hector Guzman-Orozco burden after tumor challenge IEDB https://github.com/obi-ontology/obi/issues/1594 epitope protection from tumor challenge experiment based on burden An epitope protection from tumor challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls. Hector Guzman-Orozco survival after tumor challenge IEDB https://github.com/obi-ontology/obi/issues/1594 epitope protection from tumor challenge experiment based on survival An in vivo assay measuring T cell epitope specific protection from pathogen challenge. IEDB IEDB protection from pathogen challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from pathogen challenge An in vivo assay measuring T cell epitope specific protection from tumor challenge. IEDB IEDB protection from tumor challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from tumor challenge An in vivo assay measuring T cell epitope specific protection from a challenge other than pathogen, infection, or tumor. IEDB IEDB protection from other challenge|in vivo assay in vivo assay measuring T cell epitope specific protection from other challenge An in vivo assay measuring T cell epitope specific protection from tumor challenge using survival. IEDB IEDB survival from tumor challenge|in vivo assay in vivo assay measuring T cell epitope specific survival after tumor challenge An in vivo assay measuring T cell epitope specific protection from pathogen challenge using survival. IEDB IEDB survival from pathogen challenge|in vivo assay in vivo assay measuring T cell epitope specific survival after pathogen challenge An in vivo assay measuring B cell epitope specific protection from pathogen challenge. IEDB IEDB protection from pathogen challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from pathogen challenge An in vivo assay measuring B cell epitope specific protection from tumor challenge. IEDB IEDB protection from tumor challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from tumor challenge An in vivo assay measuring B cell epitope specific protection from a challenge other than pathogen, infection, or tumor. IEDB IEDB protection from other challenge|in vivo assay in vivo assay measuring B cell epitope specific protection from other challenge An in vivo assay measuring B cell epitope specific protection from pathogen challenge using survival. IEDB IEDB survival from pathogen challenge|in vivo assay in vivo assay measuring B cell epitope specific survival after pathogen challenge An in vivo assay measuring B cell epitope specific protection from tumor challenge using survival. IEDB IEDB survival from tumor challenge|in vivo assay in vivo assay measuring B cell epitope specific survival after tumor challenge An in vivo assay measuring a T cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB protection from pathogen challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells using survival. IEDB IEDB survival after pathogen challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival An in vivo assay measuring a T cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific T cells. IEDB IEDB protection from tumor challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using survival. IEDB IEDB survival after tumor challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells based on survival An in vivo assay measuring a T cell epitope specific protection from other challenge after adoptive transfer of epitope specific T cells. IEDB IEDB protection from other challenge after adoptive transfer|in vivo assay in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells An in vivo assay measuring a B cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB protection from pathogen challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. IEDB IEDB survival after pathogen challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival An in vivo assay measuring a B cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB protection from tumor challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival. IEDB IEDB survival after tumor challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival An in vivo assay measuring a B cell epitope specific protection from other challenge after adoptive transfer of epitope specific antibodies or B cells. IEDB IEDB protection from other challenge after adoptive transfer|in vivo assay in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells An organism detection assay that identifies bacteria based on the differential retention of a crystal violet-iodine complex within the cell wall. Gram-positive bacteria retain the violet stain whereas gram-negative bacteria do not. John Judkins ORCID:0000-0001-6595-0902 American Heritage Medical Dictionary NCI https://github.com/obi-ontology/obi/issues/1603 Gram stain assay A resting arthropod trap that consists of a tent inside which an adult cow is tethered to the ground, in order to attract arthropods and collect those that rest on the interior walls of the tent. John Judkins ORCID:0000-0001-6595-0902 Sarah Kelly https://github.com/obi-ontology/obi/issues/1602 cow-baited arthropod trap A specimen that is derived from a portion of lymph collected from an organism. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB lymph specimen A specimen that is derived from part of a digestive tract. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB digestive tract specimen A T cell epitope specific cytokine production assay that detects interleukin-25 production by T cells. IEDB IEDB IL-25 release|biological activity assay measuring epitope specific interleukin-25 production by T cells A detection of specific nucleic acid polymers with complementary probes that detects interleukin-25 production by T cells. IEDB IEDB IL-25 release|RNA/DNA detection detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-25 production by T cells A flow cytometry assay that detects interleukin-25 production by T cells. IEDB IEDB IL-25 release|ICS intracellular cytokine staining assay measuring epitope specific interleukin-25 production by T cells An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells. IEDB IEDB IL-25 release|ELISA ELISA measuring epitope specific interleukin-25 production by T cells A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells. IEDB IEDB TNF release|bioassay cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells An assay kit that is manufactured by InBios International to use ELISA to test for IgM antibodies for Orientia tsutsugamushi strains Karp, Kato, Gilliam, and TA 716, with a protein microarray that has a 96-well plate and the 56-kDa type-specific antigen. John Judkins ORCID:0000-0001-6595-0902 https://inbios.com/scrub-typhus-detecttm-igm-elisa-kit-intl/ Scrub Typhus Detect IgM ELISA kit An assay kit that is manufactured by Abbott to test for IgM antibodies for Dengue with a two-plate protein microarray. One plate contains stabilized Dengue viruses 1 through 4, and the other plate contains anti-human IgM antibody. John Judkins ORCID:0000-0001-6595-0902 Panbio Dengue IgM capture ELISA kit An assay kit that is manufactured by Abbott to detect the NS1 Dengue viral protein with a protein microarray and an anti-NS1 monoclonal antibody. John Judkins ORCID:0000-0001-6595-0902 Panbio Dengue Early ELISA kit A device manufactured by Abbott for rapid detection of human IgM antibodies for Chikungunya virus in blood, using analytical chromatography. John Judkins ORCID:0000-0001-6595-0902 https://www.indiamart.com/proddetail/abbott-sd-bioline-chikungunya-igm-test-kit-12908515588.html SD Bioline Chikungunya IgM RDT kit An assay kit that is manufactured by Abbott to detect human IgM antibodies for Chikungunya with a protein microarray and ELISA. John Judkins ORCID:0000-0001-6595-0902 SD Bioline Chikungunya IgM capture ELISA kit An assay kit that is manufactured by J. Mitra to detect human IgM antibodies for Chikungunya virus with a protein microarray and double-antigen sandwich ELISA. John Judkins ORCID:0000-0001-6595-0902 Advantage Chikungunya IgM Card kit An assay that detects a type of organism and/or the quantity of individuals of a type of organism. This term is a generalized version of the term previously known as 'organism identification assay', to include classification other than species and to include quantities as outputs. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1633 organism detection assay A physical examination of an organism's ability to perform functional activities. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 functional assessment of individual An observational assessment of the loss of facial muscle tissue due to inactivity or disease. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 facial atrophy assessment An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 tongue atrophy assessment A functional assessment of an individual's ability to cough forcefully. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 forced cough assessment A functional assessment of an individual's ability to understandably repeat spoken sentences. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 speech test assessment A functional assessment of an individual's ability to touch index fingers together in front of the sternum without oscillation for a specified duration of time Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 finger to finger assessment A functional assessment of an individual's ability to touch their own nose and then touch an examiners finger in front of them and then touch their own nose once more. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 nose to finger assessment A functional assessment of an individual's ability to accurately touch a moving target with their finger and then touch their own chin a number of times in a row. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 dysmetria assessment A functional assessment of an individual's ability to alternate the forearm between pronation and suppination as quickly as possible during a specified duration of time Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 rapid alternating hands assessment A functional assessment of an individual's ability to touch their finger-tip to thumb as many times as possible during a specified duration of time. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 finger taps assessment A functional assessment of an individual's ability to slide their heel back and forth along their contralateral tibia from the patella to the ankle with the contralateral leg extended. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 heel along shin assessment A functional assessment of an individual's ability to tap their heel to the midpoint of the contralateral shin a number of times. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 heel to shin assessment An observational assesment of an individual's muscle tissue loss due to inactivity or disease. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 muscle atrophy assessment A functional assessment of an individual's ability to perform muscle movement to overcome gravity or physical resistence. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 muscle weakness assessment A functional assessment of an individual's ability to sense vibration. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 vibratory sense assessment A functional assessment of an individual's ability to sense the position of a finger or toe that has been manipulated by minimal random movements. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 position sense assessment A functional assessment of an individual's muscle contraction when a muscle is triggered by a signal from a muscle spindle in response to a stimulus applied to a specific trigger point on the body. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 deep tendon reflex assessment The functional assessment of an individual's ability to maintain balance, posture or upright stability. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 limits of stability assessment A limits of stability assessment designed to assess an individual's ability to maintain unsupported posture while sitting over a given time period. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 sitting posture assessment A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet 20 cm apart. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 stance feet apart assessment A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with their eyes closed. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 stance feet apart assessment, with eyes closed A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 stance feet together assessment A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together and eyes closed. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 stance feet together assessment, with eyes closed A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet in tandem placement. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 tandem stance assessment A limits of stability assessment designed to assess an individual's ability to maintain a stable stance on one foot. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 stance on one foot assessment A limits of stability assessment designed to assess an individual's ability to maintain balance while walking in a straight line placing steps in tandem. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 tandem walk assessment A limits of stability assessment designed to assess an individual's manner or pattern of walking. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 gait assessment A functional assessment of an individual's lower cranial nerve function via proxy of facial muscle performance. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 bulbar assessment A functional assessment of an individual's ability to articulate spoken words. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 spontaneous speech assessment A functional assessment of an individual's ability to coordinate limb movement. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 limb coordination assessment A limb coordination assessment designed to assess an individual's ability to coordinate upper limb movement. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 upper limb coordination assessment A limb coordination assessment designed to assess an individual's ability to coordinate lower limb movement. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 lower limb coordination assessment A functional assesment of an individual's nerve performance. Specifically the nerves connecting the sensory and motor structures with the central nervous system. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 nervous system functionality assessment A functional assessment of an individual's ability to maintain upright body posture. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 upright stability assessment A deep tendon reflex assessment of an individual's reaction to stimulus applied to a knee joint. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 deep tendon reflex assessment of the knee joint A physical examination of an organism through visual assesment. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 observational assessment of individual A deep tendon reflex assessment of an individual's reaction to stimulus applied to an ankle joint. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 deep tendon reflex assessment of the ankle joint A deep tendon reflex assessment of an individual's reaction to stimulus applied to a tendon of biceps brachii. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 deep tendon reflex assessment of the tendon of biceps brachii A deep tendon reflex assessment of an individual's reaction to stimulus applied to a brachioradialis. Daniel Olson, ORCID: 0000-0002-8134-1207 Critical Path Institute https://github.com/obi-ontology/obi/issues/1637 deep tendon reflex assessment of the brachioradialis A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS. A mass spectrometry assay that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules). Discussed on the OBI developer call 2022-03-07: 'tandem mass spectrometry' OBI:0200198 is under 'data transformation' but is actually defined like an assay. Moving OBI:0200198 from 'data transformation' to 'assay' is a major logical change, so the OBI development team supports obsoleting 'tandem mass spectrometry' OBI:0200198 and replacing it with ‘tandem mass spectrometry assay’ OBI:0003540. Hector Guzman-Orozco, ORCID:0000-0003-3430-8997 http://purl.obolibrary.org/obo/OBI_0200198 https://github.com/obi-ontology/obi/issues/1506 tandem mass spectrometry assay An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Orientia tsutsugamushi. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 ELISA measuring Orientia tsutsugamushi IgM antibody A microarray assay that detects the IgM antibody that binds Dengue. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 microarray assay measuring Dengue IgM antibody A microarray assay that detects NS1. John Judkins ORCID:0000-0001-6595-0902 VEuPathDB https://github.com/obi-ontology/obi/issues/1456 microarray assay measuring NS1 Analytical chromatography that detects the IgM antibody that binds Chikungunya. John Judkins ORCID:0000-0001-6595-0902