2013-05-06 Carlo Torniai Erik Segerdell Jie Zheng Karen Corday Matthew Brush Melanie Courtot Melanie Wilson Melissa Haendel Nicole Vasilevsky Scott Hoffmann Tenille Johnson en The eagle-i ontology models research resources such instruments, protocols, reagents, animal models, biospecimens. It has been developed in the context of the eagle-i project (http://eagle-i.net/) eagle-i research resource ontology editor preferred label editor preferred term GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) editor preferred term example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober example in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status OBI_0000281 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition textual definition definition GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition comment editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. GROUP:OBI:<http://purl.obfoundry.org/obo/obi> PERSON:Daniel Schober editor note definition editor definition editor term editor 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people PERSON:Daniel Schober definition editor term editor alternative term alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober alternative term definition source definition source Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 has obsolescence reason PERSON:Alan Ruttenberg PERSON:Melanie Courtot Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note is denotator type Alan Ruttenberg In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') relates an class defined in an ontology, to the type of it's denotator is denotator type imported from For external terms/classes, the ontology from which the term was imported GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Alan Ruttenberg PERSON:Melanie Courtot imported from expand expression to Chris Mungall A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" expand expression to expand assertion to A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property Alan Ruttenberg antisymmetric property part_of antisymmetric property xsd:true use boolean value xsd:true to indicate that the property is an antisymmetric property OBO foundry unique label The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . An alternative name for a class or property which is unique across the OBO Foundry. GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot has ID digit count Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" has ID range allocated to Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Person:Alan Ruttenberg Relating an ontology used to record id policy to the ontology namespace whose policy it manages term replaced by Person:Alan Ruttenberg Person:Alan Ruttenberg Use on obsolete terms, relating the term to another term that can be used as a substitute term replaced by has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. GROUP:OBI:<http://obi.sourceforge.net> PERSON:Chris Mungal has_role objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. definition needs clean up to indicate directionality has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Person:Alan Ruttenberg Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Contributor An entity responsible for making contributions to the content of the resource. Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. Coverage Coverage will typically include spatial location (a place name or geographic coordinates), temporal period (a period label, date, or date range) or jurisdiction (such as a named administrative entity). Recommended best practice is to select a value from a controlled vocabulary (for example, the Thesaurus of Geographic Names [TGN]) and that, where appropriate, named places or time periods be used in preference to numeric identifiers such as sets of coordinates or date ranges. The extent or scope of the content of the resource. Creator An entity primarily responsible for making the content of the resource. Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. Date A date associated with an event in the life cycle of the resource. Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. Description An account of the content of the resource. Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. Format The physical or digital manifestation of the resource. Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). Resource Identifier An unambiguous reference to the resource within a given context. Recommended best practice is to identify the resource by means of a string or number conforming to a formal identification system. Example formal identification systems include the Uniform Resource Identifier (URI) (including the Uniform Resource Locator (URL)), the Digital Object Identifier (DOI) and the International Standard Book Number (ISBN). Language A language of the intellectual content of the resource. Recommended best practice is to use RFC 3066 [RFC3066], which, in conjunction with ISO 639 [ISO639], defines two- and three-letter primary language tags with optional subtags. Examples include "en" or "eng" for English, "akk" for Akkadian, and "en-GB" for English used in the United Kingdom. Publisher An entity responsible for making the resource available Examples of a Publisher include a person, an organisation, or a service. Typically, the name of a Publisher should be used to indicate the entity. Relation Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a related resource. Rights Management Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource. Information about rights held in and over the resource. Source A reference to a resource from which the present resource is derived. The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. Subject and Keywords The topic of the content of the resource. Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. Title Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Resource Type The nature or genre of the content of the resource. Type includes terms describing general categories, functions, genres, or aggregation levels for content. Recommended best practice is to select a value from a controlled vocabulary (for example, the DCMI Type Vocabulary [DCMITYPE]). To describe the physical or digital manifestation of the resource, use the Format element. Ocre Definition inheres in This clarifies that only specifically dependent continuants inhere in (specifically) one independent continuant over all time. For GDCs, there in implicitly inherence to all the independent continuants in which the concretizations inhere. Should add a 'cardinality 1' restriction to the definition of specifically dependent continuant. This relation belongs in BFO/RO, and will be in BFO 2 has_contact Name of the primary person responsible for the resource. PERSON: Melissa Haendel PERSON: Melissa Haendel The lab manager who maintains an instrument in the lab. has contact has_PI PERSON: Melissa Haendel PERSON: Melissa Haendel The PI of a lab. The principle investigator of a laboratory or research project. has PI funds PERSON: Melissa Haendel PERSON: Melissa Haendel Research project that is financially supported by the organization. The NIH. is_member_of A graduate student in the lab. Identifies the organization or laboratory in which this individual is a member. PERSON: Melissa Haendel PERSON: Melissa Haendel is member of occurs_in Hibernation occurs in bears. Organism in which the biological process occurs. PERSON: Melissa Haendel PERSON: Melissa Haendel occurs in provides_access_to An access service that provides access to a flow cytometer. Instruments, reagents, organisms, or software for which the service provides access. PERSON: Melissa Haendel PERSON: Melissa Haendel change the domain tye to access service uses Here there are things to be fixed (for instance a service can use a technique...) Microsoft powerpoint is commonly used in research laboratories to prepare presentations. PERSON: Melissa Haendel PERSON: Melissa Haendel Software or protocol used by the laboratory. uses has_expertise Brian Druker has expertise in cancer research. PERSON: Melissa Haendel PERSON: Melissa Haendel Technique in which the person is proficient. has expertise has_manufacturer Organization or person that created the resource. PERSON: Melissa Haendel PERSON: Melissa Haendel Santa Cruz Biotechnology is the manufacturer of many antibodies. has manufacturer provides_service A core lab providing cell sorting to individual labs. PERSON: Melissa Haendel PERSON: Melissa Haendel Service offered by the organization. provides services specifies_the_use_of A protocol can specify the use of a flow cytometer. Instruments, techniques, reagents, organisms, or software that are referenced in a protocol. PERSON: Melissa Haendel PERSON: Melissa Haendel specifies the use of has_affiliation A researcher has an affiliation with a department. Institutional, consortia, or other organizational affiliations. PERSON: Melissa Haendel PERSON: Melissa Haendel has affiliation used_by A laboratory uses Microsoft Word. Laboratory that uses the protocol or software. PERSON: Melissa Haendel PERSON: Melissa Haendel used by has_input_type Imaging processing software that requires .jpg format files for analysis. PERSON: Carlo Torniai PERSON: Melissa Haendel Software data input format. has input format has_output_type Microsoft Excel arranges and saves data in .xlsx format. PERSON: Carlo Torniai PERSON: Melissa Haendel Software data output type. has output format achieves_objective ImageJ software measures characteristics of digital images. PERSON: Carlo Torniai PERSON: Melissa Haendel Transformation objective of the software. achieves objective has_author A journal article has authors. PERSON: Melissa Haendel PERSON: Melissa Haendel Person who authored a document. has author tobe imported probably from FOAF or anywwre according top vivo model_of Disease or condition for which the organism presents some or all defining characteristics. PERSON: Melissa Haendel PERSON: Melissa Haendel Transgenic mice are often models for a specific disease. here we need to have a more clear definition in dependence of the model model of has_topic A research project focuses on a specific topic, such as cancer research. Organism, biological process, or disease that is the subject matter of the research project or protocol. PERSON: Melissa Haendel PERSON: Melissa Haendel has topic here we need to take care of dofferent domain and is this really the same relation between research project and protocol? has_biosafety_level Level of the biocontainment precautions required to isolate dangerous biological agents in an enclosed facility. Levels range from level 1 (lowest) to 4 (highest). In the United States, the Centers for Disease Control and Prevention (CDC) specified these levels. PERSON: Melissa Haendel PERSON: Melissa Haendel Working with ebola virus has biosafety level 4. has biosafety level service_provided_by A core laboratory provides a service. Organization or laboratory performing the service. PERSON: Melissa Haendel PERSON: Melissa Haendel service provided by performs A cancer researcher performs apoptosis assays. PERSON: Melissa Haendel PERSON: Melissa Haendel Technique carried out by the person or laboratory. is_performed_by Confocal microscopy is performed by a confocal core laboratory. PERSON: Melissa Haendel PERSON: Melissa Haendel Person or laboratory that performs the service or technique. is performed by has_documentation An antibody has documentation describing attributes of the antibody. Document that contains relevant resource information. PERSON: Melissa Haendel PERSON: Melissa Haendel has documentation realizes_protocol A sequencing protocol used for next generation sequencing. PERSON: Melissa Haendel PERSON: Melissa Haendel Protocol used to perform the service. placeholder: need to be modeled for the proper kind of service (production services) realizes protocol uses_software PERSON: Melissa Haendel PERSON: Melissa Haendel Placeholder needs to be redesign Sequence analysis software. Software used to perform the service. true uses software expresses_construct A cell line that overexpresses a gene. Construct that has been introduced into the genome of a permanent cell culture. PERSON: Melissa Haendel PERSON: Melissa Haendel expresses construct related_technique Flow cytometry is a related technique for a flow cytometer instrument. Method in which the resource can be used. PERSON: Melissa Haendel PERSON: Melissa Haendel related technique recognizes_species An mouse anti-human OX40 antibody recognizes the human OX40 protein. Organism recognized by the antibody. PERSON: Melissa Haendel PERSON: Melissa Haendel recognizes species has_immunogenic_material PERSON: Melissa Haendel PERSON: Melissa Haendel Purified OX40 protein. The material used to generate an immune response to produce an antibody. For example, a tissue, a protein, or a virus. used_to_study A study of hibernation in bears. Biological process studied in the organism. PERSON: Melissa Haendel PERSON: Melissa Haendel used to study has_sequence_alteration A point mutation in a gene. A sequence variation that deviates from a canonical or reference sequence. PERSON: Melissa Haendel PERSON: Melissa Haendel has sequence alteration has_sequence_alteration has_director Name of the person who directs the organization. PERSON: Melissa Haendel PERSON: Melissa Haendel The director of a core lab. has director funded_by Organization providing financial support. PERSON: Melissa Haendel PERSON: Melissa Haendel The lab is funded by the NIH. funded by expressed_in_organism A yeast expression vector is designed to be expressed in yeast cells. Organism in which the construct is designed to be expressed. PERSON: Melissa Haendel PERSON: Melissa Haendel expressed in organism shortcut relation for participates_in_ expression process has_residency_requirement A research opportunity requires applicants to be US citizens. PERSON: Melissa Haendel PERSON: Melissa Haendel US residency status of applicants that may apply for the student research opportunity. has residency requirement related_viral_construct Construct used to generate active virus. PERSON: Melissa Haendel PERSON: Melissa Haendel The construct pWPI-GFP is used to generate GFP viral supernatants. related viral construct related_virus GFP superntants are produced by the pWPI-GFP construct. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Virus produced by viral plasmid. related virus related_research_project A research project studying breast cancer. PERSON: Melissa Haendel PERSON: Melissa Haendel Research project during which the biological specimen was collected. related research project related_biological_specimen A breast cancer specimen. Biological specimen collected as part of the research project. PERSON: Melissa Haendel PERSON: Melissa Haendel related biological specimen infects_target_organism A virus that infects human cells. Organism that the virus infects. PERSON: Melissa Haendel PERSON: Melissa Haendel infects target organism is_contact_for PERSON: Melissa Haendel PERSON: Melissa Haendel Resources for which the person is a contact. The PI is the contact for an instrument. used_to_generate_organism A construct used to generate a knockdown mouse. PERSON: Melissa Haendel PERSON: Melissa Haendel Transgenic organism generated using the construct. used to generate organism organism_generated_from_construct A construct used to generate a knockout mouse. Construct used to generate a transgenic organism. PERSON: Melissa Haendel PERSON: Melissa Haendel organism generated from construct has_preparation_technique PERSON: Melissa Haendel PERSON: Melissa Haendel Paraffin embedding of tissue. Technique used to prepare the biological specimen. has preparation technique matching_specimen Healthy breast tissue is a matching specimen for breast cancer tissue. PERSON: Melissa Haendel PERSON: Melissa Haendel Specimen match to a given biological specimen. A matched pair of biological specimens usually includes a control specimen that is either from a non-affected individual or tissue. matching specimen is_matching_specimen Healthy breast tissue is a matching specimen for breast cancer tissue. PERSON: Melissa Haendel PERSON: Melissa Haendel Specimen match to a given biological specimen. A matched pair of biological specimens usually includes a control specimen from a non-affected individual or tissue. is matching specimen has_derived_specimen DNA derived from breast cancer tissue. PERSON: Melissa Haendel PERSON: Melissa Haendel Specimen derived from another biological specimen, such as a DNA or protein isolate. has derived specimen derives_from_specimen DNA derived from breast cancer tissue. PERSON: Melissa Haendel PERSON: Melissa Haendel Specimen that is derived from another biological specimen, such as a DNA or protein isolate. derives from specimen related_cell_line Cell line collected as part of a research project. HeLa cells used for a research project. PERSON: Melissa Haendel PERSON: Melissa Haendel related cell line derives_from_material_anatomical_entity A cell line derived from a kidney. Anatomical entity from which the resource is derived. PERSON: Melissa Haendel PERSON: Melissa Haendel derives from material anatomical entity derives_from_organism A human cell line. Organism from which the resource is derived. PERSON: Melissa Haendel PERSON: Melissa Haendel derives from organism has_phase PERSON: Melissa Haendel PERSON: Melissa Haendel Phase 1 clinical trial. Phase of a clinical trial to evaluate risk and to clinically evaluate the efficacy of drugs or biologicals. has phase performs_human_study Human study performed by the organization. PERSON: Melissa Haendel PERSON: Melissa Haendel The Jackson Heart Institute performs human studies on heart disease. performs human study human_study_performed_by Jackson State University performs human studies on heart disease. Organization that performs the human study. PERSON: Melissa Haendel PERSON: Melissa Haendel human study performed by derives_from_organism_or_virus A cell line is derived from a human. Organism or virus from which the resource is derived. PERSON: Melissa Haendel PERSON: Melissa Haendel derives from organism or virus antibody_produced_by An anti-OX40 antibody is produced by a hybridoma. Hybridoma cell line used to produce the antibody. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky antibody produced by has_antibody_target A material that is recognized by an antibody. Most often this is a protein but can also include chemicals, or biological materials such as cells or organisms. Most often this is a protein but can also include chemicals, or biological materials such as cells or organisms. PERSON: Matthew Brush PERSON: Melissa Haendel ToDo: will be a subproperty of some kind of "recognizes" property. related_immunotechnique Antibody related method in which the resource can be used. Flow cytometry. PERSON: Melissa Haendel PERSON: Nicole Vasilevsky species_non_reactivity PERSON: Melissa Haendel PERSON: Nicole Vasilevsky Species in which the antibody has been shown not to cross react. author_of A journal article authored by the person. Document authored by a person. PERSON: Melissa Haendel PERSON: Melissa Haendel has_member has_format has_phenotype_biological_process has_software_license Is a legal instrument (usually by way of contract law) governing the usage or redistribution of software. PERSON: Scott Hoffmann http://en.wikipedia.org/wiki/Software_license has_phenotype_anatomical_entity has_mammalian_phenotype has_phenotype_quality has_phenotype_annotation is_PI_of A professor in the Department of Biomedical Engineering is the principal investigator (PI) of her research group and laboratory. Identifies the laboratory or research project for which this individual is the principal investigator. PERSON: Scott Hoffmann PERSON: Scott Hoffmann is PI of is_director_of A professor is the director of a consortium devoted to rare diseases. Identifies the organization for which this person is the director. PERSON: Scott Hoffmann PERSON: Scott Hoffmann is director of objective_achieved_by_operation Links an objective to a software operation whise execution achieves the objective. Is different from OBI:objective_achieved_by which links an objective to the process that achieves it. PERSON:Matthew Brush PERSON:Matthew Brush a relation between a software objective (data transformation objective) and an operation whose execution in a software tool achieves the objective software relation expanding to something like: objective_achieved_by some ('software/algorithm execution' and (specified_by some 'data processing operation')) has_specified_input 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: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input A relation between a 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. PERSON: Alan Ruttenberg see is_input_of example_of_usage has_specified_output PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output A relation between a 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. PERSON: Alan Ruttenberg is_realized_by GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] executed_during has_realization is_realized_as is_manufactured_by Alan Ruttenberg Liju Fan 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. has_make has_manufacturer 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) is_manufactured_by has_function GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall Relation between an independent continuant and a function. has_function heart has_function to-pump-blood realizes GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungal 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] 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. executes has_function_part involves_execution_of is_realization_of realizes is_specified_output_of PERSON:Bjoern Peters is_specified_output_of A relation between a 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 has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. GROUP:OBI:<http://obi.sourceforge.net> PERSON:Chris Mungal has_role achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' BP, AR, PPPB branch PPPB branch derived 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. modified according to email thread from 1/23/09 in accordince with DT and PPPB branch has grain 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 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 objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. definition needs clean up to indicate directionality produces Melissa Haendel a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. produced_by Melissa Haendel bearer_of inheres in This clarifies that only specifically dependent continuants inhere in (specifically) one independent continuant over all time. For GDCs, there in implicitly inherence to all the independent continuants in which the concretizations inhere. Should add a 'cardinality 1' restriction to the definition of specifically dependent continuant. This relation belongs in BFO/RO, and will be in BFO 2 role_of A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall role_of implements is_encoded_in adjacent_to Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum relationship agent_in relationship contained_in Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): relationship contains relationship derived_into relationship derives_from Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant. relationship has_agent relationship has_improper_part See reasons for obsoletion of improper_part_of relationship has_integral_part relationship has_part relationship has_participant Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. relationship has_proper_part relationship improper_part_of OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf] relationship integral_part_of relationship located_in Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus relationship location_of relationship part_of Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. relationship participates_in relationship preceded_by An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. relationship precedes relationship proper_part_of relationship relationship this relation was superfluous, so it has been obsoleted relationship transformation_of When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes. relationship transformed_into Obsoleted relationship DeprecatedProperty mailing_address 3181 SW Sam Jackson Park Road. Portland, OR 97239 Mailing address for correspondence. PERSON: Melissa Haendel PERSON: Melissa Haendel mailing address contact_email Email address of the primary contact. PERSON: Melissa Haendel PERSON: Melissa Haendel email last name@university.edu first_name Individual's forename. Nicole PERSON: Melissa Haendel PERSON: Melissa Haendel We refer to the Lab contact and not to the person we have contacted in order to have this informatoin first name has_inventory_number An example inventory number can be in the form: 12345 Inventory identifier for the resource. PERSON: Melissa Haendel PERSON: Melissa Haendel has inventory number has_restriction A restriction on service availability, such as university or consortium affiliation, geographical location, professional certification, or other factors. PERSON: Melissa Haendel PERSON: Melissa Haendel Resource is only available to researchers in the department. has restriction has_geographic_restriction Any service limitation tied to geographically-defined areas such as metro areas, counties, states, or regions. PERSON: Melissa Haendel PERSON: Melissa Haendel Resource is only available to researchers in Boston area. has geographic restriction last_name Individual’s surname. PERSON: Melissa Haendel PERSON: Melissa Haendel Smith We refer to the Lab contact and not to the person we have contacted in order to have this informatoin last name model_number ABI 9000 Instrument model number, which may be a name, number, or both. PERSON: Melissa Haendel PERSON: Melissa Haendel model number phone_number 503-555-5555 PERSON: Melissa Haendel PERSON: Melissa Haendel The number used to call someone by phone. phone number title Designation used to refer to an individual. PERSON: Melissa Haendel PERSON: Melissa Haendel Professor lab_data_format Current method or software used to inventory a lab's resources. Examples include Excel, index cards, FileMaker, 3-ring binder, etc. Excel spreadsheet PERSON: Melissa Haendel PERSON: Melissa Haendel lab data format lab_delivery_address Laboratory address where deliveries are made. PERSON: Melissa Haendel PERSON: Melissa Haendel Volumn Research Institute, 3rd floor, bay 1 lab delivery address version PERSON: Melissa Haendel PERSON: Melissa Haendel Software edition, typically a numeral followed by a decimal and another numeral, such as 2.1. v 1.0 operating_system Computer operating system used by the software, such as Windows, MacOS, or Linux. Microsoft Windows PERSON: Melissa Haendel PERSON: Melissa Haendel operating system has_entrez_gene_id A unique identifier assigned to each record in the Entrez Gene database. PERSON: Melissa Haendel PERSON: Melissa Haendel The entrez gene ID of mouse CD34 is 12490. has entrez gene id construct_backbone Name of the construct backbone. This label is often the first part of a construct name and refers to the part of the construct that is not the insert. PERSON: Melissa Haendel PERSON: Melissa Haendel construct backbone pENTER has_accession_number PERSON: Melissa Haendel PERSON: Melissa Haendel The accession number for a gene. Unique identifier of a biological polymer sequence (DNA, RNA, protein) when it is submitted to a sequence database. accession number has_insert_size A 40bp insert. Number of base pairs in the insert. PERSON: Melissa Haendel PERSON: Melissa Haendel insert size has_tag A FLAG tag on a protein. Expression tag that allows tracking of the RNA or protein. PERSON: Melissa Haendel PERSON: Melissa Haendel insert tag has_study_population African american study population. Characteristics of the human population being studied. May include number, demographic or geographic information, inclusion or exclusion criteria, or other descriptive information. PERSON: Melissa Haendel PERSON: Melissa Haendel study population has_CAS_number CAS number PERSON: Melissa Haendel PERSON: Melissa Haendel The CAS number for NaOH. Unique numerical identifier for a chemical as defined by the Chemical Abstracts Service (CAS). has_IUPAC_name IUPAC name International Union of Pure and Applied Chemistry (IUPAC) name of the chemical. PERSON: Melissa Haendel PERSON: Melissa Haendel The IUPAC name for NaOH. has_PubChem_CID PERSON: Melissa Haendel PERSON: Melissa Haendel PubChem CID The PubChem CID for NaOH. Unique numerical identifier for a chemical as defined by the PubChem database of chemical molecules. has_purity_grade 99.9% pure ethanol. PERSON: Melissa Haendel PERSON: Melissa Haendel Purity Grade Purity grade of a chemical reagent, often expressed in the product name by means of a quality denomination that follows to the product nomenclature, such as Guaranteed Reagent. has_url PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky The website for a manufacturer. Web address of the resource. has URL has_selectable_marker Ampicillin resistance gene. Gene that confers a trait suitable for selection. PERSON: Melissa Haendel PERSON: Melissa Haendel has selectable marker library_count 100 RNAi oligos in an oligo library. Number of elements in the library. PERSON: Melissa Haendel PERSON: Melissa Haendel library count has_uniPROT_ID PERSON: Melissa Haendel PERSON: Melissa Haendel The UniPROT ID for Mad4 protein. Unique numerical identifier for a chemical as defined by the UniProt database. has uniPROT ID has_bacterial_host_strain Bacterial strain in which the library is hosted. E.coli is used to host a DNA library. PERSON: Melissa Haendel PERSON: Melissa Haendel has bacterial host strain has_producer_strain E.coli is used to produce a DNA library. Organismal or viral strain used to produce the library. PERSON: Melissa Haendel PERSON: Melissa Haendel has producer strain has_producer_cell_type 293T cells are used to produce a lentiviral supernatant. PERSON: Melissa Haendel PERSON: Melissa Haendel Type of cell in which the virus may be produced. has producer cell type recognizes_protein_uniprot_ID PERSON: Melissa Haendel PERSON: Melissa Haendel The Uniprot ID of the gene product recognized by the antibody. The antibody recognizes a protein, with a corresponding UniProt ID. recognizes protein uniprot ID has_PubMed_ID PERSON: Melissa Haendel PERSON: Melissa Haendel PubMed ID The PMID for a journal article. Unique numerical identifier assigned to citation of life sciences and biomedical scientific journal articles in the PubMed database. has_parental_strain_name PERSON: Melissa Haendel PERSON: Melissa Haendel Parental strain name of modified organisms. Wild type 293 cells. has parental strain name has_gene_symbol CD4. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky The official symbol for the gene. has gene symbol has_affected_gene_entrez_id PERSON: Melissa Haendel PERSON: Melissa Haendel The Entrez Gene ID for the gene that is affected in a transgenic organism. The entrez gene ID of mouse CD34 is 12490. has affected gene Entrez ID has_phenotype A mouse with a shorter tail. An observable characteristic or trait of an organism, such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior (such as a bird's nest). PERSON: Melissa Haendel PERSON: Melissa Haendel has phenotype has_source A mouse house in a research lab. Organism’s source environment or clinical setting. PERSON: Melissa Haendel PERSON: Melissa Haendel has source has_infectious_history A monkey with CMV. Infectious history of the organism, such as previous viral infections that may affect the usage of the organism for research. PERSON: Melissa Haendel PERSON: Melissa Haendel has infectious history has_eligibility_requirment A grade point average above 3.5 is an eligibility requirement. PERSON: Melissa Haendel PERSON: Melissa Haendel Requirements for research opportunity eligibility. Requirements include: coursework, minimum gradepoint average, state residency, under-represented group status, field of study, or matriculation status. has eligibility requirement has_start_date Beginning time at which the research opportunity is available. January 1, 2012. PERSON: Melissa Haendel PERSON: Melissa Haendel has start date has_end_date January 21, 2012. PERSON: Melissa Haendel PERSON: Melissa Haendel Time at which the research opportunity is no longer available. has end date has_InChI_key PERSON: Melissa Haendel PERSON: Melissa Haendel The InChi key number for NaOH. Unique numerical identifier for a chemical as defined by the InChI Key database. has InChI Key has_diagnosis A biological specimen collected from a patient with breast cancer. Diagnosis of the biological specimen sampled. PERSON: Melissa Haendel PERSON: Melissa Haendel has diagnosis has_pathological_stage PERSON: Melissa Haendel PERSON: Melissa Haendel Stage IV breast cancer. Stage that has been assigned to the biological specimen, such as cancer stage, degeneration stage, normal or control. has pathological stage has_antibody_registry_ID AB12345. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky The unique ID number assigned to an antibody in the Neurosicence Information Framework (NIF) antibody registry. has antibody registry ID has_clone_ID Clone identification number assigned to a monoclonal antibody. N-262. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky has clone ID has_lot_number 4521 PERSON: Nicole Vasilevsky The identification number assigned to a particular quantity or lot of material from a single manufacturer. has lot number http://www.answers.com/topic/lot-number has_catalog_number Catalog number of a commercially manufactured reagent. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky SC-1234 has catalog number has_conjugate A molecule conjugated to the antibody, which can be used to detect the presence of the antibody. FITC. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky has conjugate target_modification PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Phosphorylation. Post-translational protein modification. target_subregion C-terminus. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky The subregion which is targeted by the antibody, such as the N- or C-terminus or a specific domain. gene_cross_reactivity Antibody cross reacts with other gene family members. Gene(s) for which the antibody has been shown to cross react. PERSON: Melissa Haendel PERSON: Nicole Vasilevsky has_sequence PERSON: Melissa Haendel PERSON: Nicole Vasilevsky Possibly import from IAO or SO. Sequence of an oligo. The sequence of nucleotide residues or amino acids in a nucleotide or a protein. has_molecular_weight PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky The molecular weight of the protein target. MRI Scanner A measurement device that visualizes detailed internal structure and limited function of the body, using a powerful magnetic field to align the nuclear magnetization of (usually) hydrogen atoms in water in the body. NMRI scanner http://en.wikipedia.org/wiki/Magnetic_resonance_imaging magnetic resonance imaging scanner nuclear magnetic resonance imaging scanner PDBML Taverna workflow format Format of Taverna workflows. HTML html, or HyperText Markup Language in full, is a data format specification is a markup language for web pages and is the publishing language of the World Wide Web. http://www.w3.org/TR/html401/ laboratory A cancer research laboratory. Material entity that performs research, provides services, or processes materials. PERSON: Melissa Haendel PERSON: Melissa Haendel requested in OBI 2894859 true core laboratory A flow cytometry core laboratory at a university. Laboratory that has the mission of providing services. Core Laboratories often charge fees for services or are funded via their affiliated organizations. PERSON: Melissa Haendel PERSON: Melissa Haendel http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Facility_Core Definition: As defined in http://dictionary.reference.com/browse/facility requested in OBI 2894859 service laboratory true instrument A flow cytometer. Material entity that is designed to have a function and play a role in scientific investigation. PERSON: Melissa Haendel See OBI listserv discussion for considerations in defining instrument. http://sourceforge.net/tracker/index.php?func=detail&aid=2894801&group_id=177891&atid=886178 http://en.wikipedia.org/wiki/Scientific_instrument instrument service offering A DNA sequencing service performed by a core lab. An information content entity that describes a service performed by a person or organization with the objective of performing a technique, providing training, providing storage of data or material entities, or providing access to resources for another person or organization Coordinate with NIF. NIF ID: nlx_res_20090105 PERSON: Melissa Haendel PERSON: Melissa Haendel service reagent A plasmid can be used as a reagent. PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). Processed material that is used in a chemical reaction or other experimental process to detect, measure, examine, or produce other substances. http://www.yourdictionary.com/reagent reagent technique A technique is a planned process used to accomplish a specific activity or task. Flow cytometry is a technique. PERSON: Melissa Haendel Protocol is added to eagle-i temporarily until a relationship between the informatio entity "protocol" and these planned processes is created. This class refers to the axtual process not the document http://en.wikipedia.org/wiki/Technique antibody reagent A reagent that is comprised of immunoglobulins produced by B cells in response to an antigen. Antibody reagents can be engineered to have specificity for specific antigens. An antibody is used to detect proteins in a Western blot assay. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://www.nlm.nih.gov/medlineplus/ency/article/002223.htm cell line Atwood et al (2000) OED of Biochemistry and Molecular Biology, Oxford University Press. Def from EFO, to be added to OBI. ; From Richard this class represents: hybridomas, stem cells{IPS/MEFs/ES}, modified standard cell lines, primary cells, unique bacterial lines, yeast lines ; Placeholder for class to be imported from the Reagent Ontology (ReO). HeLa cells are a cancer cell line that were generated from a cervical tumor. PERSON: Melissa Haendel Reagent that is a population of cells cultured in vitro that are descended through one or more generations (and possible sub-cultures) from a single primary culture which was originally derived from part of an organism. The cells of such a population share common characteristics. cell line service provider role A role inhering in a person or organization that is realized when the bearer participates in providing a service to meet the need of another person or thing. A technician in a core laboratory. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky research project A funded collection of investigations as described in a research proposal. A project to study the role of a specific protein in cell signaling. Maybe SameAs "Investigation" but is the subject of funding PERSON: Melissa Haendel PERSON: Melissa Haendel human study A clinical trial. OCRe PERSON: Melissa Haendel Research project that uses or collects measurements or assessments about humans. This should be imported from OCRE- but they currently have no generic human study type. Def is modified. human study clinical trial A clinical trial to evaluate the efficacy of a new drug. An interventional study that contains a set of procedures in medical research and drug development that are conducted to allow safety (or more specifically, information about adverse drug reactions and adverse effects of other treatments) and efficacy data to be collected for health interventions (e.g., drugs, diagnostics, devices, therapy protocols) that is performed over phases. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Clinical_trial epidemiological study A human study of diseases in populations of humans or other animals, specifically how, when and where they occur. Epidemiological studies can never prove causation, epidemiological evidence can only show that this risk factor is correlated with a higher incidence of disease in the population exposed to that risk factor. The higher the correlation the more certain the association, but it cannot prove the causation. A study of the populations and demographic of the avian flu. PERSON: Karen Corday epidemiological study http://pmep.cce.cornell.edu/profiles/extoxnet/TIB/epidemiology.html genome wide association study A genome wide association study is an examination of genetic variation across a given genome, designed to identify genetic associations with observable traits. PERSON: Karen Corday genome wide association study http://en.wikipedia.org/wiki/Genome-wide_association_study biological specimen Heart tissue obtained from an organism. Material entity that is a portion or quantity of a biological material for use in testing, examination, or study. A biological specimen can be an individual animal, a population of organisms, or is a part of or derived from an animal, plant, part of a plant, or microorganism. When a taxon is described, it is typically based on a single specimen and is referred to as the holotype. PERSON: Melissa Haendel Should have relationship to Organism biological specimen biospecimen http://en.wikipedia.org/wiki/Specimen software A general term primarily used for digitally stored data such as computer programs and other kinds of information read and written by computers. IAO is a planned specification, in SWO is an Information artifact. In eagle-i, we have a need to collect material instances and is it thus currently classified as a material entity. Microsoft Word is commonly used word processing software. PERSON: Melissa Haendel http://en.wikipedia.org/wiki/Computer_software software open source software ImageJ is open source software from the NIH, used for image quantification and analysis. PERSON: Nicole Vasilevsky Software whose source code is published and made available to the public, enabling anyone to modify it. true www.en.wikipedia.org/wiki/Open_source commercial software Microsoft Office suite is commercial software. PERSON: Nicole Vasilevsky Software that is produced for sale or that serves commercial purposes. true www.en.wikipedia.org/wiki/Commercial_software RNA sequence Data containing the arrangement of nucleotides in a DNA fragment or genome. PERSON: Nicole Vasilevsky RNA sequence The RNA sequence encodes the protein sequence. http://en.wikipedia.org/wiki/RNA protein sequence data A protein sequence data represents the primary structure of a protein and is the order in which amino acid residues, connected by peptide bonds, lie in the chain in proteins. PERSON: Karen Corday The protein sequence is encoded by the RNA sequence. http://en.wikipedia.org/wiki/Peptide_sequence protein sequence macromolecular crystallographic information data Data from the Macromolecular Crystallographic Information File (mmCIF) that is used for describing small molecule structures and associated diffraction experiments. Macromolectular Crystallographic Information data PERSON: Karen Corday http://www.sdsc.edu/pb/papers/methenz97.pdf electron density map data Data that are a three-dimensional description of the electron density in a crystal structure, determined from X-ray diffraction experiments. They describe the contents of the unit cells averaged over the whole crystal and not the contents of a single unit cell (a distinction that is important where structural disorder is present). PERSON: Karen Corday electron density map http://reference.iucr.org/dictionary/Electron_density_map NMR restraint data Data generated by NMR used as input for structure generation programs. PERSON: Nicole Vasilevsky http://www.ccpn.ac.uk/ccpn/data-model/python-api-v2-examples/nmr-restraints cell assay platform A flow cytometry set up. A platform that is an aggregate of the set of instruments and software needed to perform a cell assay procedure. Erik Segerdell PERSON: Erik Segerdell requested in OBI cell selection device A device that isolates and detects intended target cells. An autoMACS cell separator, used to separate cells tagged with magnetic beads. PERSON: Karen Corday http://www.rndsystems.com/product_detail_objectname_pluscellectkits.aspx requested in OBI electroporator A nucleofector device. An instrument that applies an electrical field to a population of cells, which causes a significant increase in the electrical conductivity and permeability of the cell plasma membrane and allows the introduction of some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA. PERSON: Erik Segerdell cell porator http://en.wikipedia.org/wiki/Electroporator requested in OBI there is a trade name 'nucleofactor' environmental control system A device or system that supports a controlled physical environment. A fume hood is an environmental control system. Erik Segerdell PERSON: Erik Segerdell requested in OBI freeze-fracture device A device that rapidly freezes a fresh tissue or cell suspension for subsequent fracture and downstream analysis. A device used to break up tumors for subsequent analysis. PERSON: Karen Corday freeze-fracture device http://en.wikipedia.org/wiki/Electron_microscope requested in OBI microfluidics platform A platform that combines several microfluidic functions (e.g. capillary valving, centrifugal pumping, and flow sequencing). An HPLC apparatus contains a microfluidics platform. Erik Segerdell PERSON: Erik Segerdell proteomics platform A platform that combines several proteomics functions. Erik Segerdell PERSON: Erik Segerdell workstation A high-end computer designed for technical or scientific applications. PERSON: Erik Segerdell computer workstation http://en.wikipedia.org/wiki/Workstation requested in OBI nucleic acid library A primer library. From Richard: RNAi, plasmid, phage, chemical, viral, [also cell libraries] ; Placeholder for class to be imported from the Reagent Ontology (ReO). PERSON: Melissa Haendel Reagent library that is a collection of DNA fragments that is stored and propagated in a population of micro-organisms through the process of molecular cloning. http://en.wikipedia.org/wiki/Dna_library nucleic acid library protein reagent An antibody is a protein reagent. PERSON: Melissa Haendel PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). Reagent that is a sequence of amino acids. peptide reagent protein reagent chemical reagent From Richard: unique rare ; Placeholder for class to be imported from the Reagent Ontology (ReO). PERSON: Melissa Haendel Reagent that is a material of pure chemical composition, either an element or a compound. Sodium hydroxide is a common chemical reagent. http://en.wikipedia.org/wiki/Chemical_substance DNA electrophoresis Electrophoresis in which DNA is separated by its resistance to movement and its charge. PCR products are subjected to DNA electrophoresis to confirm the presence of DNA. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky agarose gel electrophoresis RNA electrophoresis Electrophoresis in which RNA is separated it by its resistance to movement and its charge. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky RNA is subjected to electrophoresis in a Northern blot. protein electrophoresis Electrophoresis in which protein is separated it by its resistance to movement and its charge. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky The first step in a Western blot. high performance liquid chromatography A liquid chromatography technique that can separate a mixture of compounds and is used in biochemistry and analytical chemistry to identify, quantify and purify the individual components of the mixture. HPLC PERSON: Nicole Vasilevsky The proteins present in a sample are identified by HPLC. high pressure liquid chromatography http://en.wikipedia.org/wiki/High-performance_liquid_chromatography cell immortalization A cell culture technique where primary cell cultures are immortalized, have extended replicative capacity and grow continuously in culture with the replacement of proper growth media. Cell line generation PERSON: Nicole Vasilevsky Transformation of 293 cells. http://www.bioxys.com/i_Abm/cell_immortalization_products.htm restriction fragment length polymorphism electrophoresis A nucleic acid assay that is used to detect RFLPs, which involves fragmenting a sample of DNA by a restriction enzyme. The resulting DNA fragments are then separated by length using agarose gel electrophoresis, and transferred to a membrane via the Southern blot procedure. Hybridization of the membrane to a labeled DNA probe then determines the length of the fragments which are complementary to the probe. A RFLP occurs when the length of a detected fragment varies between individuals. PERSON: Nicole Vasilevsky RFLP electrophoresis RFLP is used in forensic science to identify a perpetrator. http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism confocal microscopy A microscopy technique used in optimal imaging that increases optical resolution and contrast of a micrograph by using point illumination and a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane. It enables the reconstruction of three-dimensional structures from the obtained images. CLSM Colocalization studies of two proteins. Confocal scanning microscopy PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Confocal_microscopy microscopy An imaging assay that uses microscopes to view samples and objects that cannot be seen with the unaided eye (objects that are not within the resolution range of the normal eye). Cell viability can be visualized by microscopy. Microscopic examination PERSON: Nicole Vasilevsky Sample microscopy http://en.wikipedia.org/wiki/Microscopy light box A device that provides a source of illumination for observation and photography of a wide variety of tests performed in virological, microbiological and clinical laboratories using either white or ultraviolet light. Coomassie stained gels can more easily be visualized using a light box. PERSON: Erik Segerdell United States Patent 4071883 cryoembedding A histological sample preparation technique involving embedding tissue in a compound that allows them to be frozen rapidly and prepares them for subsequent sectioning. Cryoembedding heart biospecimens. Frozen block cryoembedding PERSON: Nicole Vasilevsky http://www.tedpella.com/cryo_html/cryo2.htm immunohistochemistry assay A tissue/organ assay that is used to detect antigens (e.g., proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues. IHC Immunostaining PERSON: Nicole Vasilevsky Used to detect protein expression in a tissue. http://en.wikipedia.org/wiki/Immunohistochemistry light microscopy A microscopy technique that uses visible light and a system of lenses to magnify images of small samples. LM Light microscopy is used to examine cell viability. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Optical_microscopy time lapse light microscopy Light microscopy where the same object (e.g., a cell) is photographed at regular time intervals over several hours. PERSON: Nicole Vasilevsky The migration of a protein through a cell can be captured by time-lapse microscopy. http://en.wikipedia.org/wiki/Time-lapse_microscopy time lapse confocal microscopy Confocal microscopy where the same object (e.g., a cell) is photographed at regular time intervals over a specified period of time. Migration of a protein in a cell can be captured by time-lapse confocal microscopy. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Time-lapse_microscopy cryosectioning A technique used in histological sample preparation where water-rich tissues are hardened by freezing and cut in the frozen state with a freezing microtome or microtome-cryostat. Biospecimens are removed from an organism and flash frozen, then cryosectioned for subsequent histological analysis. Cryogenic sectioning Freeze sectioning Frozen sectioning PERSON: Nicole Vasilevsky cryosectioning http://www.answers.com/topic/microtome image analysis An imaging technique that allows images to be analyzed based on their pixel or voxel composition. Image analysis of bands on a gel to quantitate the relative difference in protein expression. PERSON: Melissa Haendel PERSON: Nicole Vasilevsky funding role A role inhering in a person or organization that is realized when the bearer participates in providing funding to a person or an organization for academic or business purposes. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky The NIH is a funding agency. educator role A role inhering in a person or organization that is realized when the bearer participates in providing education to a student or group of students. A teacher. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky monoclonal antibody reagent An mouse anti-human Mad4 antibody. Antibody reagent that recognizes a single epitope. PERSON: Melissa Haendel PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). polyclonal antibody reagent A rabbit anti-human SHH antibody. Antibody reagent that recognizes multiple epitopes. PERSON: Melissa Haendel PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). fluorescence and luminescence assay detection system A Licor imager, which can be used to image animals in vivo. A measurement device that detects fluorescence intensity, fluorescence polarization, time-resolved fluorescence, and luminescence, delivering information in terms of sensitivity, dynamic range, signal-to-noise, and cross-talk. PERSON: Karen Corday fluorescence and luminescence assay detection system http://www.bioresearchonline.com/product.mvc/Analyst-HTS-Assay-Detection-System-0001 laminar flow hood Device that flows filtered air onto a specially enclosed work surface. This prevents particulate and microbial contamination, while protecting the user from the potential exposure to infectious material being handled. PERSON: Karen Corday Tissue culture work is usually done in a laminar flow hood. http://www.cybersight.org/bins/content_page.asp?cid=1-1581-1642 laminar flow cabinet laminar flow hood dispensing well plate A nanodispenser that is used for the massive parallel delivery of liquid volumes in the range of 50 nL. DWP PERSON: Erik Segerdell Plate replicator. dispensing well plate doi:10.1016/j.sna.2004.05.038 robot arm A mechanical instrument that consists of an upper arm link and a lower arm link that are interconnected by a uniaxial joint. The upper arm link is connected with a structure via a universal joint. PERSON: Karen Corday http://www.google.com/patents/about?id=ZqcsAAAAEBAJ robot arm compressor A device that transfers energy to a gaseous fluid for the purpose of raising the pressure of the fluid as is the case when the compressor is the prime mover of the fluid through the process. Gresh, M.T. (2001). Compressor performance: aerodynamics for the user. Woburn, MA: Butterworth-Heinermann. PERSON: Karen Corday compressor vacuum centrifuge concentrator A centrifuge that includes a vacuum chamber within which a centrifuge rotord is rotatably mounted for spinning a plurality of vials containing a solution at high speed while subjecting the solution to a vacuum condition for concentration and evaporation. A speed vac is used to concentrate a sample. PERSON: Nicole Vasilevsky http://www.google.com/patents/about?id=J7Q6AAAAEBAJ&dq=4226669 sample concentrator speed vac speed vacuum vacuum centrifuge concentrator refrigerated centrifuge A centrifuge that can be operated at low temperatures. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Used to prepare protein lysates. biological safety cabinet A fume hood. An instrument used for containment of biological materials, which functions as a primary barrier to prevent the escape of biological aerosols into the laboratory environment. PERSON: Karen Corday biological safety cabinet biosafety cabinet http://www.drs.illinois.edu/bss/factsheets/cabinets.aspx transmission electron microscope An electron microscope that uses a high voltage electron beam to create an image. For use in imaging of biological molecules. PERSON: Karen Corday http://en.wikipedia.org/wiki/Electron_microscope#Transmission_electron_microscope_.28TEM.29 transmission electron microscope fluorescence microscope An optical microscope used to study properties of organic or inorganic substances using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption. Epifluorescence microscope Fluorescent microscope PERSON: Karen Corday Used to visualize biomolecules. fluorescence microscope http://en.wikipedia.org/wiki/Fluorescence_microscope UV crosslinker A UV crosslinker is used to crosslink RNA to a membrane in Northern blots. An instrument designed to crosslink molecules, such as DNA or RNA to a surface, such as a membranes. PERSON: Nicole Vasilevsky UV crosslinker http://research.amnh.org/molecular/equipment_folder/Stratalinker%201800.pdf automatic sputter coater A sputter coater where the complete sequence of flush, leak, coat and vent is automatically controlled. The solenoid operated leak valve allows the gas pressure to return automatically to pre-set conditions. For gold deposition of scanning electron microscopy specimens. PERSON: Karen Corday automatic sputter coater http://www.canemco.com/catalog/instruments/Sputter-coaters.htm#Automatic_Sputter_Coater_ industrial robot A device that is programmable, multifunctional, and mechanical that is designed to move material, parts, tools, or specialized devices through variable programmed motions to perform a variety of tasks. PERSON: Karen Corday Robotic arm moving pin array for moving compounds. http://www.osha.gov/dts/osta/otm/otm_iv/otm_iv_4.html plate sealer A mechanical instrument that applies seal material on top of microplates (plates) to seal individual wells. A plate sealer is used to seal plates for real-time PCR. PERSON: Karen Corday http://www.chem.agilent.com/Library/usermanuals/Public/G5402-90001_PlateLocUG_EN.pdf plate sealer barcode labeler An instrument that prints bar code labels and applies them to a product, such as to the side of a microplate. PERSON: Karen Corday bar code labeler http://cp.chem.agilent.com/Library/usermanuals/Public/G5404-90001_LabelerUG_EN.pdf chip reader An instrument used to detect and record data provided by a microarray chip. PERSON: Nicole Vasilevsky http://www.sciclips.com/sciclips/protein-biomarker-protocol.do?protocol=Ciphergen%20ProteinChip%20SELDI-TOF-MS%20Analysis&type=8166 ultrasonic cell disruptor A device that uses ultrasound to disrupt cell membranes and release cellular contents. An ultrasonic cell disruptor is used to break up bacteria during protein purification. PERSON: Karen Corday http://en.wikipedia.org/wiki/Sonication ultrasonic cell disruptor fluidics station An instrument used for the wash and stain operation of arrays. PERSON: Nicole Vasilevsky Wash and stain functions on an automated immunohistochemistry instrument. http://www.affymetrix.com/browse/products.jsp?productId=131439&navMode=34000&navAction=jump&aId=productsNav#1_1 cell storage device A CO2 incubator. Device that has the function of maintaining cell lines, primary cultures or cell isolates in a viable state. PERSON: Melissa Haendel PERSON: Melissa Haendel cell storage device fermentor A bioreactor that provides a sterilie environment, ideal for growth of any bacteria, yeast, or fungi. A bioreactor used to produce monoclonal antibodies from a hybridoma. PERSON: Nicole Vasilevsky bioreactor fermentor http://www.nbsc.com/bioflo510.aspx fluorescence spectrometer A spectrophotometer that analyzes fluorescence from a sample. It uses a beam of light, usually ultraviolet light, to excite the electrons in molecules of certain compounds and causes them to emit light of a lower energy, typically, but not necessarily, visible light. Can be used to quantify DNA. PERSON: NIcole Vasilevsky fluorescence detector fluorescence spectrometer http://en.wikipedia.org/wiki/Fluorescence_spectroscopy amino acid analyzer A high performance liquid chromatography instrument that is used to detect free amino acids automatically by reacting the free amino acids, under basic conditions, with phenylisothiocyanate (PITC) to produce phenylthiocarbamyl (PTC) amino acid derivatives. An amino acid analyzer can be used to determine the composition of a protein. PERSON: Karen Corday amino acid analyzer http://www.protein.iastate.edu/aaa.html peptide synthesizer A device that produces peptides, which are organic compounds in which multiple amino acids are linked via peptide bonds. A peptide synthesizer is used to generate peptides to be used as antigens in immune models. PERSON: Karen Corday http://en.wikipedia.org/wiki/Peptide_synthesizer peptide synthesizer mass spectrometer sample spotter A mass spectrometer sample spotter can be used to identify proteins in a sample. An instrument designed to automatically mix and spot digested proteins and matrix onto any MALDI MS targets. PERSON: Nicole Vasilevsky http://www.gelifesciences.com/aptrix/upp01077.nsf/content/Products?OpenDocument&parentid=976027&moduleid=165591&zone=Elpho mass spectrometer sample spotter environmental scanning electron microscope A scanning electron microscope that has a secondary-electron detector capable of operating in the presence of water vapour and pressure-limiting apertures with differential pumping in the path of the electron beam to separate the vacuum region (around the gun and lenses) from the sample chamber, which allows samples to be observed in low-pressure gaseous environments (e.g. 1-50 Torr) and high relative humidity (up to 100%). Fungal spores in lemon grass leaf can be imaged using an environmental scanning electron microscope. PERSON: Nicole Vasilevsky environmental scanning electron microscope http://en.wikipedia.org/wiki/Scanning_electron_microscope#Environmental_SEM nanoindenter An instrument used for indentation hardness tests for nanoindentation, a method for measuring and testing very small volumes of mechanical properties. PERSON: Karen Corday http://en.wikipedia.org/wiki/Nanoindenter nanoindenter nano universal testing machine A device that is used to measure tensile and bending properties of microscopic materials. PERSON: Karen Corday http://mms.postech.ac.kr/ nano universal testing machine nano-UTM microscope digital camera A digital camera for a microscope, which records image data of a sample image obtained by the microscope in a recording medium. A digital camera hooked up to a microscope, which can be used to capture the images that are visualized by the microscope. PERSON: Karen Corday http://www.google.com/patents/about?id=XumGAAAAEBAJ microscope digital camera cell separator A FACS machine can be used to sort cell populations. An instrument that detects and isolates target cells from a mixed population of cells. Fisher, D., et al. (Eds.). (1998). Cell separation: a practical approach. Oxford: Oxford University Press. http://books.google.com/books?id=GSWudM-1XGcC PERSON: Nicole Vasilevsky cell separator genomic library A cDNA library for the mouse genome. A construct library that carries the entire genome of a source organism. PERSON: Karen Corday Placeholder for class to be imported from the Reagent Ontology (ReO). genomic library http://en.wikipedia.org/wiki/Genomic_library RNAi library A RNAi library for a gene of interest, such as SHH. Nucleic acid library that is comprised of small interfering RNA molecules. PERSON: Melissa Haendel PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). RNAi library cDNA construct library A cDNA library expressing fragments from the mouse genome. A construct library that is a collection of cDNA plasmids. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). cDNA library http://en.wikipedia.org/wiki/CDNA_library miRNA library PERSON: Melissa Haendel PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). RNAi library that is comrpised of microRNA (21-22 nucelotides). miRNAs are endogenous post-transcriptional regulators that bind to complementary sequences in the three prime untranslated regions (3' UTRs) of mRNA, usually resulting in gene silencing. Each miRNA may repress hundreds of mRNAs. miRNA libraries are NOT in expression vectors but are directly transfected into cells. miRNA libraries can be used to screen for target drugs. miRNA library siRNA library An siRNA library may be used to knockdown gene expression to study the function of that gene. PERSON: Melissa Haendel PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). RNAi library that is comprised of small (20-25 nucleotides) interfering RNA or silencing RNA that targets mRNA for degradation. siRNAs are synthetic double-stranded RNA. siRNA libraries are NOT in expression vectors. The siRNAs are directly transfected into cells. siRNA library shRNA library An shRNA library may be used to knockdown gene expression to study the function of that gene. PERSON: Melissa Haendel PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). ; this is an expression library, and has part some construct RNAi library that is comprised of small hairpin RNA or short hairpin RNA that target mRNA for degradation. shRNAs are single stranded RNAs containing a tight hairpin turn and are synthesized and inserted into (primarily) Viral Cloning vectors. When expressed in the cell the loop is degraded and what is left is the siRNA (ds RNA) part. shRNA library construct A reagent that is a virus or DNA molecule capable of autonomous replication, used as a vehicle to transfer foreign genetic material into a host cell. A construct may contain an insert of DNA from an external source, and may be used for cloning or for expression purposes. Cells are transfected with constructs expressing a gene of interest to study the gene function. PERSON: Matthew Brush PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). construct vector BAC An artificial chromosome vector that contains portions of the bacterial fertility plasmid (F-plasmid). Used for transforming and cloning in bacteria, usually E. coli. BAC Often used to sequence the genome of organisms in genome projects. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). bacterial artificial chromosome http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome YAC An artificial chromosome containing chromosomal features needed for replication and preservation in yeast cells (origin, telomere, and centromere). A YAC is built using an initial circular plasmid, which is typically broken into two linear molecules using restriction enzymes to allow ligation of a sequence or gene of interest and form a single large linear piece of DNA. YACs are useful for the physical mapping of complex genomes and for the cloning of large genes. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). YAC http://en.wikipedia.org/wiki/Yeast_artificial_chromosome yeast artificial chromosome PAC An artificial chromosome derived from the genome of the P1 bacteriophage. Used for transforming and cloning in bacteria, usually E. coli. PAC PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome cosmid A hybrid plasmid that contains cos DNA sequences derived from the Lambda bacteriophage, which allow for DNA packaging in phage capsids for delivery by viral transduction. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). cosmid http://en.wikipedia.org/wiki/Cosmid fosmid A hybrid plasmid that contains sequences from the bacterial F-plasmid to enable packaging in lambda phage for delivery by viral transduction. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). fosmid http://en.wikipedia.org/wiki/Fosmid peptide library PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). Reagent library that contains a great number of peptides that have a systematic combination of amino acids. Usually, a peptide library is synthesized on solid phase, mostly on resin, which can be made as flat surface or beads. http://en.wikipedia.org/wiki/Peptide_library peptide library chemical library A library of kinase inhibitors. PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). Reagent library that is a collection of stored chemicals. Each chemical has associated information stored in some kind of database with information such as the chemical structure, purity, quantity, and physiochemical characteristics of the compound. chemical library http://en.wikipedia.org/wiki/Chemical_library yeast two-hybrid library A library used to screen interacting proteins. An expression library that is a collection of yeast two hybrid constructs. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/Two-hybrid_screening yeast two-hybrid library yeast two-hybrid construct A construct that can be used to detect protein-protein interactions. A construct used for yeast two hybrid screening assays, which is engineered to express a protein of interest fused to either the DNA-binding domain (BD) fragment or activation domain (AD) of a transcription factor. Yeast two hybrid constructs are typically plasmids or phagemids. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/Two-hybrid_screening transgenic lambda phage A lambda phage expressing a gene of interest. A transgenic virus derived from a lambda phage that is engineered to serve as a vehicle to carry foreign genetic material, which it can transfer into cells or organisms. PERSON: Matthew Brush http://en.wikipedia.org/wiki/Vector_%28molecular_biology%29 lambda phage vector phage display peptide library A peptide library that contains phage display, an expression system of peptides, at the surface of phage particles. The construction of a phage display library is accomplished by the incorporation of the nucleotide sequence encoding the peptide to be displayed into a phage genome as a fusion to a gene encoding a phage coat protein. The fusion of the protein with the phage coat protein ensures that the peptide to be displayed is presented at the surface of the mature phage, while the sequence encoding it is contained within the same phage particle, allowing a physical link between the phenotype and genotype of the expressed peptide. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://www.phagedisplay.net/ phage display peptide library combinatorial peptide library A peptide library synthesized through combinatorial chemistry techniques. PERSON: Matthew Brush Placeholder for class to be imported from the Reagent Ontology (ReO). combinatorial peptide library http://www.genomicglossaries.com/content/libraries_synthesis.asp overlapping peptide peptide library A peptide library in which peptide sequences are engineered to exhibit a specified degree of overlap with other peptides in the library. The library generation process is characterized by two parameters, fragment length and offset number, each library is generated by breaking the original protein or peptide into many equal-length overlapping fragment, each has 8 to 20 residues in size. PERSON: Matthew Brush Placeholder for class to be imported from the Reagent Ontology (ReO). http://www.genscript.com/overlapping_library.html overlapping peptide peptide library alanine scanning peptide library A peptide library containing peptides in which each non-alanine residue is substituted one at a time with an alanine residue, allowing determination of each residue's contribution to the peptides functionality. Alanine scanning library is able to identify specific amino acid residues responsible for the peptide's function, stability, and conformation. PERSON: Matthew Brush Placeholder for class to be imported from the Reagent Ontology (ReO). alanine scanning peptide library http://www.genscript.com/alanine_scanning.html natural product extracts chemical library A chemical library that consists of chemicals produced by and extracted from living organisms. A natural products extracts chemical library can be used to screen for drug targets. PERSON: Matthew Brush PERSON: Matthew Brush Placeholder for class to be imported from the Reagent Ontology (ReO). known bioactives collection chemical library A chemical library that consists of chemicals known to exert a biological effect in living organisms or cells. PERSON: Matthew Brush PERSON: Matthew Brush Placeholder for class to be imported from the Reagent Ontology (ReO). synthetic chemical library A chemical library that consists solely of synthetic chemicals. PERSON: Matthew Brush PERSON: Matthew Brush Placeholder for class to be imported from the Reagent Ontology (ReO). IgG PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgA PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgA has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical alpha heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgD PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgD has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical delta heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgE PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgE has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical episilon heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgM PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgM has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical mu heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgG1 PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG1 has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 1 heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgG2 PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG2 has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 2 heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgG2a PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG2a has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 2a heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgG2b PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG2b has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 2b heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgG2c PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG2c has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 2c heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgG3 PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG3 has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 3 heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm IgG4 PERSON: Nicole Vasilevsky The antibody isotype that is a glycoprotein molecules that are produced by plasma cells in response to an immunogen and which function as antibodies. IgG4 has a four chain structure as the basic unit. They are composed of two identical light chains (23kD) and two identical gamma 4 heavy chains (50-70kD). http://pathmicro.med.sc.edu/mayer/IgStruct2000.htm biosafety level A biosafety level is the level of the biocontainment precautions required to isolate dangerous biological agents in an enclosed facility. The levels of containment range from the lowest biosafety level 1 to the highest at level 4. PERSON: Karen Corday Work with ebola virus is a biosafety level 4. biosafety level http://en.wikipedia.org/wiki/Biosafety_level antibody isotype A subtype of antibodies. In placental mammals there are five antibody isotypes known as IgA, IgD, IgE, IgG and IgM. The "Ig" prefix that stands for immunoglobulin, another name for antibody, and differ in their biological properties, functional locations and ability to deal with different antigens. IgG is a common antibody isotype for monoclonal antibodies. PERSON: Nicole Vasilevsky To be defined differently as subtype of antibody http://en.wikipedia.org/wiki/Antibody#Isotypes ultratome A microtome that can allow for the preparation of extremely thin sections. The linear thermal expansion of the mounting is used to provide very fine control of the thickness allowing for extremely thin cuts, which are especially important for use with transmission electron microscope (TEM). PERSON: Melissa Haendel Samples analyzed by transmission electron microscopy are prepared using an ultratome. http://en.wikipedia.org/wiki/Microtome#Ultramicrotome ultramicrotome two-photon confocal microscope A confocal microscope that uses laser-excited autofluorescence and second harmonic signals that can be analyzed to construct a three dimensional, microanatomical, structural image. PERSON: Karen Corday Used for imaging of biological samples. http://web.mit.edu/solab/Documents/Assets/Navarro-2P-A%20nondestructive%20method%20for%20studying%20wound%20healing.pdf two-photon confocal microscope DNA quantitation assay A nucleic acid assay that is used to quantify the amount of DNA. PERSON: Melissa Haendel PERSON: Melissa Haendel Quantitating DNA after a plasmid preparation, using a spectrophotometer. nucleic acid labeling A labeling technique whereby nucleic acids are labeled with radioisotopes, fluorophores, or other molecular entities for the purposes of tracking nucleic acids in an experimental system. PERSON: Melissa Haendel PERSON: Melissa Haendel mRNA fluorophore labeling for use in microarray analysis. instrumentation technical support PERSON: Melissa Haendel Process whereby technical expertise is given regarding design, repair, upkeep, or by building instruments. Technical support for computer software. Technical support to use a flow cytometer. http://en.wikipedia.org/wiki/Instrumentation electron microscopy A microscopy technique that produces an electronically-magnified image of a specimen for detailed observation. The electron microscope (EM) uses a particle beam of electrons to illuminate the specimen and create a magnified image of it. The microscope has a greater resolving power than a light-powered optical microscope, because it uses electrons that have wavelengths about 100,000 times shorter than visible light (photons), and can achieve magnifications of up to 2,000,000x, whereas light microscopes are limited to 2000x magnification. Cell structure can be examined by electron microscopy. Diagnostic electron microscopy EM PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Electron_microscope transmission electron microscopy An electron microscopy technique whereby a beam of electrons are transmitted through an ultra thin specimen, interacting with the specimen as it passes through. An image is formed from the interaction of the electrons transmitted through the specimen; the image is magnified and focused onto an imaging device, such as a fluorescent screen, on a layer of photographic film, or to be detected by a sensor such as a CCD camera. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Transmission_electron_microscopy scanning electron microscopy A type of electron microscopy that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity. PERSON: Nicole Vasilevsky SEM Used to image biomolecules. http://en.wikipedia.org/wiki/Scanning_electron_microscope oligonucleotide synthesis Biomolecule synthesis of relatively short fragments of nucleic acids with defined chemical structure (sequence). PERSON: Karen Corday Production of primers. http://en.wikipedia.org/wiki/Oligonucleotide_synthesis oligonucleotide synthesis microcapillary electrophoresis Electrophoresis designed to separate species based on their size to charge ratio in the interior of a small microcapillary filled with an electrolyte. PERSON: Karen Corday The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins and cells on a single platform. http://en.wikipedia.org/wiki/Capillary_electrophoresis microcapillary electrophoresis video Data containing moving pictures stored in digital and analog formats. PERSON: Carlo Torniai http://en.wikipedia.org/wiki/Video gel image An image of an agarose gel stained with Ethidium bromide. Images that are obtained from gels, such as polyacrylamide or agarose gels used to analyze protein or DNA. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky ion trap mass spectrometer A mass spectrometer that uses three electrodes to trap ions in a small volume. The mass analyzer consists of a ring electrode separating two hemispherical electrodes. A mass spectrum is obtained by changing the electrode voltages to eject the ions from the trap. The ion-trap mass spectrometer has a compact size and the ability to trap and accumulate ions to increase the signal-to-noise ratio of a measurement. PERSON: Erik Segerdell http://www.chemistry.adelaide.edu.au/external/soc-rel/content/ion-trap.htm ion trap mass spectrometer cell staining DAPI stain to stain nuclei. PERSON: Melissa Haendel PERSON: Melissa Haendel Staining that involves the application of dye to cells. virus plaque assay A virus plaque assay is performed to determine viral titers of viral supernatants, that are used to infect cells to study gene function. An organismal assay that is used to determine viral titers. PERSON: Melissa Haendel Plaque assay http://www.biology-online.org/dictionary/Plaque_assay virus replication assay purification Material processing whereby one material is separated into a pure fraction from one or more other materials. PERSON: Melissa Haendel Purification of a protein. http://www.biology-online.org/dictionary/Purification virus plaque purification PERSON: Melissa Haendel Plaque assay Production of viral supernatants to study a specific gene. Purification that is used to purify viral entities. http://www.biology-online.org/dictionary/Plaque_assay RNA quantitation assay An nucleic acid assay that is used to quantify the amount of RNA. PERSON: Melissa Haendel PERSON: Melissa Haendel nested polymerase chain reaction Amplification of a fragment of DNA. Nested PCR PERSON: Melissa Hanedel Polymerase chain reaction that involves two sets of primers, used in successive runs of polymerase chain reaction whereby the second set of primers is intended to amplify a secondary target within the first run product. http://en.wikipedia.org/wiki/Nested_polymerase_chain_reaction viral DNA extraction Extraction of DNA from an input material that specifically isolates viral DNA. PERSON: Melissa Haendel PERSON: Melissa Haendel inverted microscope An optical microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. Cell lines can be visualized using an inverted microscope. PERSON: Karen Corday http://en.wikipedia.org/wiki/Inverted_microscope inverted microscope experimental posttranslational modification Chemical modification of a protein after translation in an experimental setting. Experimental phosphorylation of a protein. Experimental post-translational modification Experimental post-translational protein modification Experimental post-translational protein processing Experimental protein modification Experimetnal PTM PERSON: Karen Corday http://en.wikipedia.org/wiki/Posttranslational_modification posttranslational modification protein identification A protein assay performed to identify the sequence of proteins in a molecule. Mass spectrometry is a method for protein identification. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky protein identification intervention A planned process used to influence one or more factors in a research study, and the independent variable in an interventional study wherein the influence is measured or evaluated. An drug intervention for cancer. PERSON: Melanie Wilson PERSON: Melissa Haendel case-only study A Dictionary of Epidemiology, Fifth Edition, Edited by Miquel Porta. p. 33. ISBN:978-0-19-531449-6 http://prsinfo.clinicaltrials.gov/definitions.html Observational study whereby there is a single group of individuals with specific characteristics. This is a method that analyzes data from a case series and is used in case-crossover studies, in case-specular designs, and in molecular and genetic epidemiology to assess relationships between environmental exposures and genotypes. PERSON: Melissa Haendel case-only study nucleotide-free workbench A PCR workstation. PCR workstation PERSON: Melissa Haendel This device provides effective decontamination of solutions, reagents and equipment before carrying out sensitive PCR reactions or other nucleotide-free operations. http://www.prohealthservicezone.com/Customisation/News/Analysis_Inspection_and_Laboratory/PCR_equipment/Safety_certified_PCR_workstation.asp water purification system A portable water purifier. Device that is used to purify water of contaminants. PERSON: Melissa Haendel There are likely numerous subtypes here, but this maybe too granular for our needs. http://www.millipore.com/lab_water/clw4/tutorial&tabno=5 water purification system blinded outcome assessor role A role inhering in a person or organization that is realized when the bearer participates in accessing the outcomes of a blinded study. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky blinded outcome assessor role blinded caregiver role A role inhering in a person or organization that is realized when the bearer participates in providing care to a patient without knowledge of the type of treatment or intervention that is used, such as blinding in a clinical trial. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky blinded caregiver role blinded investigator role A role inhering in a person or organization that is realized when the bearer performs a study without knowledge of the type of treatment or intervention that is used, such as blinding in a clinical trial. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Randomized_controlled_trial blinded subject role A patient is given a treatment, but is unaware if it is the placebo or actual drug. A role inhering in a person or organization that is realized when the bearer participates in a study, such as a clinical trial but is not aware of the type of treatment or intervention that is used. PERSON: Nicole Vasilevsky blinded subject role http://en.wikipedia.org/wiki/Randomized_controlled_trial open blinded study An interventional study in which the person collecting the data and the subject know whether the subjects are in the control or experimental groups. Open trial Open-label trial PERSON: Nicole Vasilevsky http://medical-dictionary.thefreedictionary.com/single-blind+study open blinded study single blinded study An interventional study in which the person collecting the data knows whether the subjects are in the control or experimental groups but the subjects do not. PERSON: Nicole Vasilevsky http://medical-dictionary.thefreedictionary.com/single-blind+study single blinded study double blinded study An interventional study in which neither the subjects of the experiment nor the persons administering the experiment know the critical aspects of the experiment; a double-blind procedure is used to guard against both experimenter bias and placebo effects. PERSON: Nicole Vasilevsky double blinded study http://www.thefreedictionary.com/double-blind+study hemocytometer A cytometer used for visual counting of cells in a blood sample or other fluid under a microscope. PERSON: Nicole Vasilevsky The number of viable cells can be counted on a hemocytometer after trypan blue staining. http://www.google.com/search?q=hemocytometer&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-US:official&client=firefox-a#hl=en&client=firefox-a&hs=9NX&rls=org.mozilla:en-US:official&q=hemocytometer&tbs=dfn:1&tbo=u&sa=X&ei=HX1BTqT0BezViAL324WVBQ&ved=0CBYQkQ4&bav=on.2,or.r_gc.r_pw.r_cp.&fp=a5190ac754b40f6f&biw=1505&bih=751 manual cytometer automatic cytometer A coulter counter is a commonly used automatic cytometer. A cytometer that automatically counts and sizes particles and cells by detecting changes in electrical conductance of a small aperture as fluid containing cells are drawn through. PERSON: Tenille Johnson automatic cell counter coulter counter http://en.wikipedia.org/wiki/Coulter_counter viability analyzer controller A device that interfaces with a peripheral device. This may be a link between two parts of a computer (for example a memory controller that manages access to memory for the computer) or a controller on an external device that manages the operation of (and connection with) that device. A memory controller that manages access to memory for the computer. PERSON: Tenille Johnson http://en.wikipedia.org/wiki/Controller_%28computing%29 CO2 incubator A incubator that controls the carbon dioxide (CO2) content of the atmosphere inside. Carbon dioxide incubator PERSON: Tenille Johnson Used to store and house cell lines and cultures. http://en.wikipedia.org/wiki/Co2_incubator stereotaxic device A head is positioned in a stereotaxic device, prior to brain surgery. Device that immobilizes and positions an organism such that surgery may be performed using an external, three-dimensional frame of reference, usually based on the Cartesian coordinate system. PERSON: Melissa Haendel http://www.thefreedictionary.com/stereotaxic stereotaxic device stereotaxic lab standard dual stereotaxic device PERSON: Melissa Haendel PERSON: Melissa Haendel Stereotaxic device which allows positioning of two organisms simultaneously. dual stereotaxic device dual stereotaxic lab standard http://www.kopfinstruments.com/Stereotaxic/902.htm single stereotaxic device PERSON: Melissa Haendel PERSON: Melissa Haendel Positioning a head in a stereotaxic device prior to brain surgery. Stereotaxic device which allows positioning of a single organism. single stereotaxic device single stereotaxic lab standard microtome cryostat Histological sections are cut using a microtome cryostat. Microtome that cuts frozen tissue within a temperature controlled frozen environment. PERSON: Melissa Haendel PERSON: Melissa Haendel microtome cryostat anesthesia induction chamber An inhalation chamber that used to anesthetize organisms that allows for controlled exposure to the anesthesia while eliminating personnel exposure to anesthetic gas. Mice are placed in an anesthesia induction chamber, for administration of anesthesia. PERSON: Melissa Haendel anesthesia induction chamber http://www.ezanesthesia.com/ez_anesthesia/index.html infrared spectrophotometer Infrared spectroscopy is used in quality control, dynamic measurement, and monitoring applications such as the long-term unattended measurement of CO2 concentrations in greenhouses. PERSON: Melissa Haendel Spectrophotometer that has a prism or grating for the study and recording of infrared spectra. It usually consists of a radiation source such as a Nernst glower, a monochromator, a detector, an amplifier and a recorder. http://www.photonics.com/directory/dictionary/Definition.aspx?type=2&DictionaryID=4754 infared spectrophotometer infrared spectrophotometer intravenous injection IV injection Injection of a substance into the vein of an organism. PERSON: Melissa Haendel PERSON: Melissa Haendel Tail vein injection into a mouse. intravenous injection deconvolution microscope Fluorescence microscope that uses a computational method to reduce out-of-focus fluorescence in three-dimensional (3D) microscope image. McNally et al., Methods. 1999 Nov;19(3):373-85. PMID: 10579932 PERSON: Nicole Vasilevsky Used to image biological samples. deconvolution microscope gavage Administration of a drug into an animal via gavage. Agent delivery of substances by means of a small plastic tube passed through the nose or mouth into the stomach, not explicitly 'forcibly'. Enteral tube feeding Gastrogavage PERSON: Karen Corday Tube feeding gavage http://en.wikipedia.org/wiki/Force-feeding intraperitoneal injection IP IP injection Injection of a substance into the body cavity. Injection of a substance into the peritoneal cavity. PERSON: Karen Corday http://en.wikipedia.org/wiki/Intraperitoneal_injection i.p. i.p. injection intraperitoneal injection subcutaneous injection Injection of a a bolus into the subcutis, the layer of skin directly below the dermis and epidermis, collectively referred to as the cutis. Injection of a solution into the scruff of the neck of a rodent. PERSON: Karen Corday S.C. injection SC injection Sub cu injection http://en.wikipedia.org/wiki/Subcutaneous_injection subcutaneous injection surgery A material processing technique that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury or to help improve bodily function or appearance. PERSON: Karen Corday Surgical removal of a mole. http://en.wikipedia.org/wiki/Surgery surgery NMR spectra data NMR spectra data NMR spectra is the intensity of the NMR signal as a function of frequency. Nuclear magnetic resonance spectra data PERSON: Karen Corday http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance NMR-based metabolite profiling A nuclear magnetic resonance assay used for profiling of metabolites (a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism) using nuclear magnetic resonance. NMR-based metabolite profiling PERSON: Karen Corday http://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=201425 gas chromatography-mass spectrometry platform A mass spectrometer that combines the gas-liquid chromatography and mass spectrometry to identify different substances within a test sample. Can be used for protein identification and characterization. GC-MS platform GC/MS platform PERSON: Karen Corday gas chromatography-mass spectrometry platform http://en.wikipedia.org/wiki/Gas_chromatography-mass_spectrometry electrocardiogram A physiological assay that is a transthoracic interpretation of the electrical activity of the heart over time captured and externally recorded by skin electrodes. It is a noninvasive recording produced by an electrocardiographic device. An electrocardiogram is used to measure heart function. ECG PERSON: Karen Corday electrocardiogram http://en.wikipedia.org/wiki/Electrocardiography cardiac output measurement A physiological assay that measures cardiac output, which is the volume of blood being pumped by the heart, in particular by a ventricle in a minute. Methods of measurement range from direct intracardiac catheterisation to non-invasive measurement of the arterial pulse. An echocardiogram. PERSON: Karen Corday cardiac output measurement http://en.wikipedia.org/wiki/Cardiac_output echocardiogram A physiological assay that uses standard ultrasound techniques to take two-dimensional pictures of the cardiovascular system and can produce accurate assessment of the velocity of blood and cardiac tissue at any arbitrary point using pulsed or continuous wave Doppler ultrasound. Cardiac US scan Diagnostic ultrasound of heart Echocardiographic procedure Echocardiography PERSON: Karen Corday US scan of heart Ultrasonic cardiography Ultrasonography of heart Ultrasound of heart Used to study heart function. cardiac ECHO echocardiogram http://en.wikipedia.org/wiki/Echocardiography invasive hemodynamic measurement A physiological assay that measures simultaneously acquired and processed blood flow and blood pressure via the placement of invasive catheters into the vasculature. PERSON: Karen Corday Pollack, A. N. (Ed.) (2011). Critical care transport. Sudbury, MA: Jones and Bartlett. ISBN: 978-0- 7637-1223-5. http://books.google.com/books?id=cuWoyV19dq8C invasive hemodynamic measurement data acquisition A technique that samples real world physical conditions and conversion of the resulting samples into digital numeric values that can be manipulated by a computer. Acquisition of flow cytometry data. DAQ PERSON: Karen Corday data acquisition http://en.wikipedia.org/wiki/Data_acquisition tail vein injection Adoptive transfer of cells via tail vein. An intravenous injection of a substance into the lateral tail vein of an organism, usually a mouse or rat. PERSON: Karen Corday http://www.lab-manual.com/lm_383.htm tail vein injection mouse breeding A laboratory animal care technique performed to produce offspring of laboratory mice by pairing mice as mating pairs. Breeding methods include selective breeding, which is the systematic breeding of animals in order to change certain qualities in them, inbreeding, which is the breeding of genetically related mice, and strain breeding, which concentrates on a certain mouse and its offspring, usually involving moderate inbreeding. Breeding transgenic mice. PERSON: Karen Corday http://www.hiiret.fi/eng/breeding/index.html mouse breeding access service A service offering that describes a service in which the 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. Allowing access to a microscope in a core lab. Coordinate with NIF PERSON: Matt Brush PERSON: Matthew Brush storage service A computer server. A service offering that describes a service in which the consumer provides some material or data as input which a service provider stores and returns as output. PERSON: Matt Brush PERSON: Matthew Brush coordinate with NIF. NIF ID:nlx_res_20090419 training service A service offering that describes a service in which the provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer Coordinate with NIF. NIF ID: nlx_res_20090444 PERSON: Matt Brush PERSON: Matthew Brush Training a researcher to use a microscope. material processing service A service offering that describes a service in which the 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 Biopsy service. Coordinate with NIF: NIF ID: nlx_res_20090416 PERSON: Nicole Vasilevsky http://neurolex.org/wiki/Category:Production_service_resource material analysis service An analysis service offering that describes a service in which the 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. Coordinate with NIF: NIF ID: nlx_res_20090420 Flow cytometry analysis of T cells. PERSON: Nicole Vasilevsky http://neurolex.org/wiki/Category:Analysis_service_resource material production service A material processing service offering that describes a service in which the provider makes physical changes to a specified input material that produce a new entity as specified output that is returned the service consumer. The specified output of a material production service can be contained within, derived from, or synthesized from specified input materials, but it represents a material entity that is of a distinct type from any of the specified input materials. Coordinate with NIF. NIF ID: nlx_res_20090418 PERSON: Matthew Brush Production of monoclonal antibodies from a hybridoma. http://neurolex.org/wiki/Category:Material_service_resource biobank picking station An instrument comprised of a number of -80 C storage units with liquid carbon dioxide back-up and a centralized automated picking station that reads the 2D barcodes on all tubes and re-arrays any requested samples at 15 C. PERSON: Bob Garces Samples can be requested and easily retrieved from a biobank picking station. Zuo, D., et al. (2006). PlasmID: a centralized repository for plasmid clone information and distribution. Nucleic Acids Research, Database issue D1-D5. DOI:10.1093/nar/gkl898 (http://nar.oxfordjournals.org/cgi/screenpdf/gkl898v1) barcode reader An instrument that is used to electronically read printed barcodes PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Barcode_reader cellular assay An assay that generates data about the presence, quantity, structure, function, behavior, or activity of cells, or a process that occurs at a cellular level of anatomical granularity (includes subcellular structures and organelles). Flow cytometry. PERSON: Matthew Brush PERSON: Nicole Vasilevsky cell analysis data storage A data transformation technique that involves the process of recording or retrieving information or data. Information storage PERSON: Karen Corday Storing data on a server. bulk data storage data storage http://en.wikipedia.org/wiki/Data_storage research data storage construct insert A gene, such as p53. PERSON: Melissa Haendel Reagent that is part of a construct comprised of DNA from an external source. construct insert http://www.answers.com/topic/dna-construct immunofluorescence microscopy assay An imaging assay that allows for detection and visualization of the location and relative abundance of any protein in cells or tissues by microscopy using fluorescent tagged antibodies. Fluorescent immunoassay IF IMF IMF assay Immunofluorescence assay Labeling of proteins using fluorescent-tagged antibodies. PERSON: Nicole Vasilevsky http://www.bio.davidson.edu/courses/genomics/method/IMF.html gas chromatography-mass spectrometry metabolite profiling A mass spectrometry assay used for the screening of apparent or novel metabolic phenotypes in functional genomic studies of plants or microbes. Can be used for protein identification and characterization. GC-MS based metabolite profiling GC/MS metabolite profiling Kopka, J. (2006). Current challenges and developments in GC-MIS metabolite profiling technology. Journal of Biotechnology, 123, 312-322. PMID: 16434119 PERSON: Karen Corday protein-ligand interaction assay A protein interaction detection assay used to study protein-ligand interactions. An assay to determine if myoglobin binds to its ligand, heme. PERSON: Tenille Johnson http://en.wikipedia.org/wiki/Protein_ligand ligand binding analysis protein-ligand interaction assay single-nucleotide polymorphism analysis A SNP in the F5 gene causes a hypercoagulability disorder with the variant Factor V Leiden. A nucleic acid assay used to detect single nucleotide variations in a nucleotide sequence. PERSON: Nicole Vasilevsky SNP analysis http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism microsatellite analysis A nucleic acid assay used method for detection of chromosomal deletions by loss of heterozygosity studies and for detection of microsatellite instability. DNA fingerprining DNA profiling ; STR analysis ; Short tandem repeat analysis Forensic genetic analysis Genetic fingerprinting Microsatellite instability analysis PERSON: Karen Corday STR profiling Short tandem repeat profiling Used for genetic analysis. Wild, P. J. et al. (2004). Laser microdissection for microsatellite analysis in colon and breast cancer. In G. I. Murray and S. Curran (Eds.), Laser capture microdissection: methods and protocols. New York: Springer. doi/10.1385/1-59259-853-6:093 embryonic stem cell culture Cell culture of embryonic stem cells, which were derived from embryos in vitro. ES cell culture Mouse embryonic fibroblast cells. PERSON: Karen Corday http://stemcells.nih.gov/info/basics/basics3.asp embryonic stem cell electroporation ES cell electroporation Electroporation in embryonic stem cells to overexpress a protein of interest. PERSON: Karen Corday Transfection of a gene into stem cells. http://en.wikipedia.org/wiki/Electroporation targeted homologous recombination Antibody generation in B cells. Experimental genetic modification that uses homologous recombination to change an endogenous gene. The method can be used to delete a gene, remove exons, add a gene, and introduce point mutations. Genetic engineering Genome manipulation Homologous recombination PERSON: Karen Corday http://en.wikipedia.org/wiki/Gene_targeting embryo transplantation A material processing technique in which eggs from female animals are mixed with sperm from male animals. After the egg is fertilized and divides into an embryo, the embryo is split into identical embryos, and implanted in separate female surrogates, and allowed to develop normally. Can be used to generate transgenic mice strains. Embryo transfer PERSON: Karen Corday Paul, N. (2002). Science for you: biology. Cheltenham: Nelson Thomas Ltd. (http://books.google.com/books?id=gTWbFq3gCPUC) environmental chamber An anesthesia chamber for rodents. An environment control instrument used to test the effects of specified environmental conditions on biological samples, industrial products, materials, and electronic devices and components. An environmental chamber can be used as a stand-alone test for environmental effects on test specimens, as preparation of test specimens for further physical tests or chemical tests, or as environmental conditions for conducting testing of specimens. PERSON: Tenille Johnson environmental chamber http://en.wikipedia.org/wiki/Environmental_chamber charge-coupled device camera A digital camera that is designed to convert optical brightness into electrical amplitude signals using a plurality of CCDs, and then reproduce the image of a subject using the electric signals without time restriction. CCD camera Can be used in medical imaging. PERSON: Tenille Johnson charge-coupled device camera http://www.electronics-manufacturers.com/products/digital-photography/ccd-camera/ charge-coupled device detector A charged-coupled device camera used for medical imaging. A photodetector that senses light or other electromagnetic energy using a charge coupled device (CCD), which detects the movement of electrical charge, usually from within the device to an area where the charge can be manipulated. CCD detector PERSON: Tenille Johnson charge-coupled device detector http://en.wikipedia.org/wiki/Charge-coupled_device blastocyst injection Injection into blastocysts (pre-implantation embryos), which are isolated from donor females and microinjected with genetically modified embryonic stem (ES) cells. PERSON: Karen Corday Production of transgenic mice. http://www.imbim.uu.se/resource/Blastocystinjection.html transfection reagent A chemical reagent that introduces foreign DNA into a eukaryotic cell. Lipofectamine is a commonly used transfection reagent. PERSON: Karen Corday Placeholder for class to be imported from the Reagent Ontology (ReO). http://www.iscid.org/encyclopedia/Transfection_Reagents BAC library A BAC library containing the mouse genome. A genomic library that contains discrete collections of host bacteria, each of which carries a DNA insert from a source organism cloned into a BAC construct, such that the collection of cloned DNA molecules represents the entire genome of the source organism. This term can also represent the collection of BAC constructs prior to their delivery into the host cells. BAC library PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/Genomic_library expression library A construct library that contains expression vectors, which are used to express a specific protein. An expression library to isolate genes that could confer antibiotic resistance. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). expression library http://en.wikipedia.org/wiki/Expression_cloning expression construct A construct that is designed to be expressed in insect cells. A construct that is engineered to produce large amounts of stable messenger RNA, and therefore proteins in a specific cell type. The construct often contains regulatory sequences that act as enhancer and promoter regions and lead to efficient transcription of the gene carried on the expression vector. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). expression construct http://en.wikipedia.org/wiki/Expression_vector PAC library A genomic library that contains discrete collections of host bacteria, each of which carries a DNA insert from a source organism cloned into a PAC construct, such that the collection of cloned DNA molecules represents the entire genome of the source organism. This term can also represent the collection of PAC constructs prior to their delivery into the host cells. PAC library PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/Genomic_library fosmid library A genomic library that contains discrete collections of fosmid constructs carrying DNA inserts from a source organism, such that the collection of DNA inserts represents the entire genome of the source organism. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). fosmid library http://en.wikipedia.org/wiki/Fosmid YAC library A genomic library that contains discrete collections of host yeast cells, each of which carries a DNA insert from a source organism cloned into a YAC construct, such that the collection of cloned DNA molecules represents the entire genome of the source organism. This term can also represent the collection of YAC constructs prior to their delivery into the host cells. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/Genomic_library cosmid library A genomic library that contains discrete collections of cosmid constructs carrying DNA inserts from a source organism, such that the collection of DNA inserts represents the entire genome of the source organism. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). cosmid library http://homepages.strath.ac.uk/~dfs99109/BB211/GenomicLibrary.html lambda phage library An organism library containing trangenic lambda phage. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). lambda phage library cold room Instrument that consists of insulated room and refrigeration components that together maintain the room at a constant temperature below room temperature. PERSON: Melissa Haendel PERSON: Melissa Haendel Walk-in refrigerator. cold room walk-in refridgerator chemical fume hood A chemical fume hood is used when working with highly volatile chemicals. Instrument that is a local ventilation device that is designed to limit the user's exposure to hazardous or noxious fumes, vapors or dusts. A fume hood is typically a large piece of equipment enclosing five sides of a work area, the bottom of which is most commonly located at a standing work height. Air is drawn in from the front (open) side of the cabinet, and either expelled outside the building or made safe through filtration and fed back into the room. PERSON: Melissa Haendel chemical fume hood fume hood http://en.wikipedia.org/wiki/Fume_hood tissue culture incubator A CO2 incubator designed to house cell cultures. An incubator that is used in tissue culture rooms for culturing primary cells, cell lines, or tissues. PERSON: Erik Segerdell http://www.medterms.com/script/main/art.asp?articlekey=18426 tissue culture incubator liquid nitrogen dewar A cryostat that is used for biomedical storage of samples using liquid nitrogen as a refrigerant. A dewar that is used for long-term storage of cell line stocks. PERSON: Erik Segerdell PERSON: Erik Segerdell liquid nitrogen dewar liquid nitrogen tank photometer A photometer is used to quantitate the concentration of DNA in a sample. An instrument for measuring light intensity or optical properties of solutions or surfaces. Photometers are used to measure iIlluminance, irradiance, light absorption, scattering of light, reflection of light, fluorescence, phosphorescence, and luminescence. PERSON: Karen Corday http://en.wikipedia.org/wiki/Photometer recombinant protein production Material production of proteins that have been produced by recombinant DNA techniques, which allows the production of large quantities of recombinant protein. PERSON: Nicole Vasilevsky Production of recombinant insulin. http://www.wisegeek.com/what-is-recombinant-protein-production.htm 2D gel spot exciser 2D gel spot exciser 2D spot picker A spot cutter that is used to excise spots from two-dimensional (2D) electrophoretic gels. Gel excision of a 2D gel, for subsequent protein analysis. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Two-dimensional_gel_electrophoresis frequency counter A coulter counter is used to count the number of cells in a sample. A device that is used for measuring frequency, which is defined as the number of events of a particular sort occurring in a set period of time. PERSON: Erik Segerdell frequency counter http://en.wikipedia.org/wiki/Frequency_counter pulmonary function tests A physiological assay used to measure the ability of the lungs take in and release air and the ability to move gases such as oxygen from the atmosphere into the body's circulation. Lung function tests PERSON: Tenille Johnson PFT Tests to detect decreased lung capacity. http://www.nlm.nih.gov/medlineplus/ency/article/003853.htm pulmonary function tests spirometry A pulmonary function test used to measure lung function, specifically the measurement of the amount (volume) and/or speed (flow) of air that can be inhaled and exhaled. Bronchospirometry PERSON: Nicole Vasilevsky Spirogram http://en.wikipedia.org/wiki/Spirometry spirometry gas diffusion tests A pulmonary function test that measures the amount of oxygen and other gases that cross the lungs' air sacs (alveoli ) per minute. These tests evaluate how well gases are being absorbed into a person's blood from their lungs. PERSON: Tenille Johnson gas diffusion tests http://www.webmd.com/lung/lung-function-tests body plethysmography A pulmonary function test that may be used to measure: total lung capacity (TLC), which is the total amount of air your lungs can hold, or residual volume (RV), which is the amount of air that remains in your lungs after you exhale as completely as possible. Body box plethysmography PERSON: Tenille Johnson Total body plethysmography Whole body plethysmography body plethysmography http://www.webmd.com/lung/lung-function-tests inhalation challenge tests A pulmonary function test done to measure the response of a person's airways to substances that may be causing asthma or wheezing. Inhalation bronchial challenge testing PERSON: Tenille Johnson Provocation studies http://www.webmd.com/lung/lung-function-tests inhalation challenge tests exercise stress tests A pulmonary function test done to evaluate the effect of exercise on lung function tests. Spirometry readings are done after exercise and then again at rest. Exercise stress tests are often performed after a heart attack. Exercise test Exercise tolerance test PERSON: Tenille Johnson exercise stress tests http://www.webmd.com/lung/lung-function-tests multiple-breath washout test A pulmonary function test performed to check lung function in patients with cystic fibrosis. PERSON: Tenille Johnson http://www.webmd.com/lung/lung-function-tests multiple-breath washout test spirometer A spirometer is an apparatus for measuring the volume of air inspired and expired by the lungs. It is a precision differential pressure transducer for the measurements of respiration flow rates. The spirometer records the amount of air and the rate of air that is breathed in and out over a specified period of time. PERSON: Tenille Johnson http://en.wikipedia.org/wiki/Spirometer spirometer objective lens An instrument that contains an optical element that gathers light from the object being observed and focuses the light rays to produce a real image, using either a single lens or combinations of several optical elements. Objective lenses are used in microscopes, telescopes, cameras, slide projectors, CD players and many other optical instruments. An objective lens of a microscope. PERSON: Tenille Johnson http://en.wikipedia.org/wiki/Objective_lens object glass objective objective glass objective lens video camera A camera used for electronic motion picture acquisition. Creation of home videos using a video camera. PERSON: Tenille Johnson camcorder http://en.wikipedia.org/wiki/Video_camera video camera ELISPOT microplate reader A plate reader used to count the colored spots that are formed in the course of ELISPOT assays. An ELISPOT microplate reader can be used to measure protein expression in samples. ELISPOT microplate reader PERSON: Tenille Johnson http://en.wikipedia.org/wiki/Plate_reader flow cytometry list mode data Data containing raw cytometer data files that list the values of the scatter and fluorescence parameters for each event in the order in which the events passed through the cytometer's interrogation point (usually a laser beam). Most cytometers create listmode files in the Flow Cytometry Standard (FCS) format, which is not understood by general purpose scientific software. Converting a listmode file to a plain text ASCII format enables it to be read by such software, or viewed and edited with a word processor. PERSON: Tenille Johnson http://www.umass.edu/microbio/mfi/ascii.htm listmode file irradiation system An instrument that contains a shielded cabinet system and is used to irradiate biological specimens. An x-ray irradiator. PERSON: Tenille Johnson http://www.kimtronmedical.com/IC160.html irradiation system urine analyzer A device used for urinalysis testing. An instrument to detect glucose levels in urine. PERSON: Tenille Johnson http://en.wikipedia.org/wiki/Urine_test_strip#Automated_Urine_Test_Strip_Analyzers urine analyzer ultraviolet transilluminator An instrument that consists of a light box that emits ultraviolet light, used for visualization of agarose and polyacrylamide gels. DNA gels stained with ethidium bromide are visualized using a UV transilluminator. PERSON: Nicole Vasilevsky http://www.topac.com/transilluminators.html orbital shaker An instrument that consists of a platform and racks to hold tubes, which continually shakes in an orbital motion, which is used to mix liquids. Depending on the model, the instrument may be located on a counter or on the floor. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Used to shake bacterial cultures, to promote growth. environmental shaker atomic force microscope A scanning force microscope used for determining the surface topography of native biomolecules at subnanometer resolution. It allows biomolecules to be imaged not only under physiological conditions, but also while biological processes are at work. AFM PERSON: Karen Corday Surface topologies with nano-scale roughness (cleaved silicon, e.g.) can be resolved an atomic force microscope. http://www.mih.unibas.ch/Booklet/Booklet96/Chapter3/Chapter3.html goniometer A device that either measures angle or allows an object to be rotated to a precise angular position. A protractor. PERSON: Karen Corday http://en.wikipedia.org/wiki/Goniometer scanning auger electron microprobe A measurement instrument used to determine the elemental composition of conductive and semiconductive surfaces, in which a highly focused and energetically well-defined electron beam is incident on the sample. Electrons ejected from the sample are analyzed in terms of their kinetic energy and quantity. Enhanced lateral spatial resolution for elemental analysis. PERSON: Nicole Vasilevsky http://www.physics.montana.edu/ical/instrumentation/auger.asp explosion-proof refrigerator A cooling appliance used for the safe storage of volatile materials that need to be kept cold, but not freezing. A refrigerator used to store volatile chemicals. PERSON: Tenille Johnson explosion-proof refrigerator http://www.wisegeek.com/what-is-an-explosion-proof-refrigerator.htm explosion-proof freezer A cooling appliance used for the safe storage of volatile materials that need to be kept frozen. PERSON: Tenille Johnson Volatile chemicals may be stored in an explosion-proof freezer. explosion-proof freezer http://www.wisegeek.com/what-is-an-explosion-proof-refrigerator.htm microforge A microforge is used to produce micropipettes, used for microinjection. Instrument designed for the fabrication and processing of glass micropipettes and other related microtools for use in patch pipette tip polishing, tip size reduction (for holding pipettes), contact stretching (large tip sharpening), tip bending, tip sealing, in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), and pipette production in a variety of pipette configurations. PERSON: Tenille Johnson http://www.tritechresearch.com/narishige-needle-overview.html microforge microinjector A device which provides the pressure that is needed to deliver a sample solution from a micropipette into cells. PERSON: Tenille Johnson The effects of a drug on an individual cell can be tested by microscope-assisted dosage with a microinjector. http://en.wikipedia.org/wiki/Microinjectors microinjector natural product extraction Extraction of a biological entity to purify a chemical or biochemical entity or mixture of entities. PERSON: Melissa Haendel PERSON: Melissa Haendel Purification of DNA from a blood sample. natural product extraction bioactivity assay A molecular assay that tests the activity of a chemical or biological reagent to affect a biological system. Overexpression of a plasmid expressing a gene, in a cell culture, to confirm the gene has biological activity in the system. PERSON: Melissa Haendel PERSON: Melissa Haendel bioactivity assay chemical synthesis CS Chem syn Chemical compounding Material production technique whereby chemical entities are synthesized from other chemical entities. PERSON: Melissa Haendel PERSON: Melissa Haendel Synthesis of aspirin. chemical synthesis nucleic acid preparation station An instrument used for automated, high-throughput extraction of nucleic acids from samples. PERSON: Nicole Vasilevsky http://www.autogen.com/product_autogenprep965.htm atomic spectrophotometer A spectrophometer used for the qualitative and quantitative determination of chemical elements employing the absorption of optical radiation (light) by free atoms in the gaseous state. PERSON: Nicole Vasilevsky Soil samples from an industrial site can be tested for the presence of mercury using an atomic spectrophotometer. http://en.wikipedia.org/wiki/Atomic_absorption_spectroscopy liquid handling Agent delivery of a selected quantity of reagents, samples or other liquids to a designated container. An ELISA plate washer. PERSON: Karen Corday http://en.wikipedia.org/wiki/Liquid_handling_robot rheometer An instrument used to measure the way in which a liquid, suspension or slurry flows in response to applied forces. It is used for those fluids which cannot be defined by a single value of viscosity. PERSON: Karen Corday http://en.wikipedia.org/wiki/Rheometer tissue embedding A sample preparation technique where cells or tissue are placed in a supporting medium. The medium can be paraffin wax (paraffin embedding) or plastics (plastic embedding) such as epoxy resins. A technique performed prior to tissue sectioning and histology. PERSON: Nicole Vasilevsky http://www.biology-online.org/dictionary/Tissue_embedding tissue sectioning Histological sample preparation of tissue, to cut it into thin sections, usually using a microtome or a cryostat, for further analysis. PERSON: Nicole Vasilevsky Preparation of brain slices for subsequent histological analysis. http://books.google.com/books?id=svzyJdQVsaEC, Burry, R. W. (2010). Immunocytochemistry: a practical guide for biomedical research. New York: Springer. needle grinder A device used to sharpen hypodermic needles. PERSON: Tenille Johnson http://www.freepatentsonline.com/5495988.html needle grinder inertial impact drill A drill that is designed to operate in conjunction with micropipettes, microelectrodes, and micromanipulators used for microinjection into cells for diverse applications in cytology. The action of the inertial impact drill is like that of a miniature jackhammer. PERSON: Nicole Vasilevsky http://www.findthatpatent.com/Inertial_impact_drill_for_cytological_applications,6251658.html hematology analyzer A measurement device used to perform complete blood counts, erythrocyte sedimentation rates (ESRs), or coagulation tests. Blood samples taken from patients are analyzed using a hematology analyzer. PERSON: Tenille Johnson haematology analyser hematology analyzer http://en.wikipedia.org/wiki/Automated_analyzer#Haematology_analysers blood gas analyzer A blood anlayzer used to measure the pH and the partial pressures of oxygen and carbon dioxide in arterial blood, as well as calculate the bicarbonate concentration. PERSON: Tenille Johnson blood gas analyzer http://en.wikipedia.org/wiki/Arterial_blood_gas infrared microscope A microscope that uses the infrared region of the electromagnetic radiation spectrum, often used for the study of materials that are uniformly transparent or opaque in the visible spectrum, but have significant absorption or transmission bands in the 700 nanometer-plus wavelength region. A specimen that is opaque to visible light, such as a blade of grass can be visualized through its thickness by way of its response to infrared light with the use of an infrared microscope. PERSON: Nicole Vasilevsky http://www.microscopyu.com/articles/optics/objectivespecial.html upright microscope A microscope that has the illumination system below the stage and the lens system above the stage. An upright microscope is used to view cell lines growing in a flask. PERSON: Karen Corday http://science.howstuffworks.com/light-microscope5.htm PCR/UV workstation An instrument that uses UV irradiation as a sterilizer to provide a clean workspace to set up PCR reactions. The UV irradiation breaks down DNA sequences so that replication cannot occur in subsequent amplification processes. PCR reactions are set up in a PCR/UV workstation. PERSON: Karen Corday http://www.thistlescientific.co.uk/acatalog/thermal_details/BCUVSC_details.html electromyography A physiological assay used to evaluate and record electrical activity produced by skeletal muscles. Can be used for musculoskeletal evaluations. EMG PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Electromyography treadmill Exercise equipment used for running or walking while staying in one place. The machine provides a moving platform with a wide conveyor belt and an electric motor or a flywheel. PERSON: Karen Corday http://en.wikipedia.org/wiki/Treadmill pulse pressure injector An instrument used to produce gas pressure pulses to an injection pipette. PERSON: Karen Corday http://www.asiimaging.com/pdfs/MPPI-2_Manual.pdf slide drying oven An oven that is used for rapid drying of histology slides, typically consisting of a drying chamber, digital temperature and time controller, and internal fan. PERSON: Erik Segerdell PERSON: Erik Segerdell slide drying oven tissue drying oven automatic coverslipper An automatic coverslipper can be used to prepare slides for microscopic examination. An material transfer instrument that is used to automatically apply a glass coverslip to a microscope slide. PERSON: Erik Segerdell United States Patent 3833449 automatic coverslipper cover slipper 3T MRI scanner 3 Tesla MRI scanner 3 Tesla magnetic resonance imaging scanner 3T MR system 3T MRI scanner 3T MRI system 3T magnetic resonance imaging scanner A 3T MRI scanner is used to evaluate brain function. An MRI scanner with a magnet strength of 3 Tesla. PERSON: Erik Segerdell http://www.urmc.rochester.edu/radiology/ digitizing tablet An instrument that allows one to hand-draw images and graphics, similar to the way one draws images with a pencil and paper. PERSON: Karen Corday graphics tablet http://en.wikipedia.org/wiki/Graphics_tablet nucleic acid isolation Material component separation of nucleic acids from biological samples, for research purposes such as cloning or gene expression analysis. PERSON: Nicole Vasilevsky Plasmid purification from a bacterial culture. http://acad.erskine.edu/facultyweb/baker/J05-10_DNA%20Technology/Isolation%20of%20Nucleic%20Acids.doc auger electron spectroscopy A materials assay used specifically in the study of surfaces and, more generally, in the area of materials science. Underlying the spectroscopic technique is the Auger effect, as it has come to be called, which is based on the analysis of energetic electrons emitted from an excited atom after a series of internal relaxation events. High resolution secondary electron analysis. PERSON: Karen Corday http://en.wikipedia.org/wiki/Auger_electron_spectroscopy atomic force microscopy AFM Force microscopy Imaging of biomolecules. Microscopy used to determine the surface topography of native biomolecules at subnanometer resolution. It allows biomolecules to be imaged not only under physiological conditions, but also while biological processes are at work. PERSON: Nicole Vasilevsky Scanning force microscopy http://en.wikipedia.org/wiki/Atomic_force_microscopy multicapillary electrophoresis system A 96-well capillary sequencer, used to perform high-throughput analysis of samples. A capillary electrophoresis instrument containing multiple capillaries, at least one source for the emission of a beam intended to to excite molecules lying in its path and inside the capillaries and means for detecting the fluorescence of the molecules exited by said beam, used for automated analysis of DNA fragments and RNA. PERSON: Nicole Vasilevsky http://www.google.com/patents?id=7I93AAAAEBAJ tissue microarrayer A manual or automated arrayer that is used to precisely assemble tissue cores, as small as 0.6 mm in diameter, in paraffin blocks for tissue microarray analysis. PERSON: Erik Segerdell http://en.wikipedia.org/wiki/Tissue_microarray tissue microarrayer tissue specimen profile Data that describe a clinical tissue specimen, e.g. a tissue profile for new gene and protein targets or a molecular profile for tissue specimens or diseases provided by tissue microarray technology. PERSON: Erik Segerdell PMID:11257096 tissue information tissue specimen profile X-ray powder diffraction spectrometer A spectrophotometer that uses monochromatic x-rays to determine the interplanar spacings of the unknown crystalline materials for identification and characterization. Samples are analyzed as powders with grains in random orientations to insure that all crystallographic directions are "sampled" by the beam. PERSON: Nicole Vasilevsky http://www.physics.montana.edu/ical/instrumentation/xrd.asp crystallization A material processing technique that is the (natural or artificial) process of formation of solid crystals precipitating from a solution, melt or more rarely deposited directly from a gas. Crystallization is also a chemical solid-liquid separation technique, in which mass transfer of a solute from the liquid solution to a pure solid crystalline phase occurs. PERSON: Karen Corday Protein structures are determined by crystallization analyses. http://en.wikipedia.org/wiki/Crystallization x-ray photoelectron spectroscopy A spectrophotometry technique that measures the elemental composition, empirical formula, chemical state and electronic state of the elements that exist within a material. XPS spectra are obtained by irradiating a material with a beam of X-rays while simultaneously measuring the kinetic energy and number of electrons that escape from the top 1 to 10 nm of the material being analyzed. Electron spectroscopy for chemical analysis PERSON: Karen Corday X ray photoelectron spectroscopy XPS http://en.wikipedia.org/wiki/X-ray_photoelectron_spectroscopy phosphorimager An image acquisition device that uses storage phosphor technology in life science imaging applications. PERSON: Nicole Vasilevsky Phosphorimaging of a Western blot. http://imagers.salk.edu/pimager/pimFAQ.html phosphoimager multi-imager A gel imager with light and UV filters. An image acquisition instrument that captures digital images from single- and multiple-color fluorescence, chemiluminescence, chemifluorescence, and colorimetric samples. PERSON: Karen Corday http://ricfacility.byu.edu/fluors.html scanning electron microscope An electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity. PERSON: Karen Corday SEM Used to image biomolecules. http://en.wikipedia.org/wiki/Scanning_electron_microscope X-ray diffraction sample cooler A device used for X-ray diffraction and designed for cooling inorganic, small-molecule and macromolecular crystals for X-ray crystallography. Cryostream PERSON: Karen Corday http://journals.iucr.org/d/issues/2000/03/00/me0093/me0093bdy.html water softener An instrument used to reduce the dissolved calcium, magnesium, and to some degree manganese and ferrous iron ion concentration in hard water. PERSON: Karen Corday Water softener is used in places where the water is hard, to make it more drinkable. http://www.isws.illinois.edu/chem/psl/Softeners.asp mechanical stage A device that can be mounted on the microscope stage and which allows for precise adjustments of the slide. A mechanical stage on a microscope. PERSON: Karen Corday http://www.labessentials.com/microscope-accessories.htm#Mechanical%20Stage hematocrit centrifuge A centrifuge used for the determination of volume fraction of erythrocytes in blood. Blood samples that are taken from patients are subjected to hematocrit centrifugation for subsequent analysis. PERSON: Karen Corday http://www.hettichlab.com/appc/content_manager/page.php?ID=160009&dbc=dr0aavhds5jr9hmleoh2k5ske3 protein purification A protein of interest may be isolated from a bacterial culture overexpressing the protein by protein purification methods. A purification process intended to isolate a single type of protein from a complex mixture. PERSON: Karen Corday Protein separation http://en.wikipedia.org/wiki/Protein_purification polisher An mechanical instrument that enables precise sample thinning and polishing of a wide range of materials. PERSON: Nicole Vasilevsky http://www.cns.fas.harvard.edu/facilities/tool_detail.php?MID=20 operant conditioning chamber An animal cage that is used in the study of both operant conditioning and classical conditioning. The structure forming the shell of a chamber is a box large enough to easily accommodate the organism being used as a subject. It is often sound-proof and light-proof to avoid distracting stimuli. Operant chambers have at least one operandum (or "manipulandum"), and often two or more, that can automatically detect the occurrence of a behavioral response or action. An operant conditioning chamber is used to study behavior in mice or rat models after treatment with certain drugs to determine their effect on behavior. PERSON: Tenille Johnson Skinner box http://en.wikipedia.org/wiki/Operant_conditioning_chamber operant conditioning chamber motorized stage A mechanical stage using motorized controls. A microscope stage. PERSON: Tenille Johnson PERSON: Tenille Johnson motorized stage animal activity data Animal activity data may be recorded after an experimental procedure. Data pertaining to the activity of laboratory animals or animals in an experimental setting. PERSON: Tenille Johnson PERSON: Tenille Johnson animal activity data animal activity monitoring system A blood pressure monitor. An animal physiology monitoring system used to monitor the specific behavior of animals in an experimental setting. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky animal activity monitor animal activity monitoring system behavioral locomotive activity chamber arterial blood gas test A hematology assay that measures the acidity (pH) and the levels of oxygen and carbon dioxide in the blood from an artery. This test is used to check how well the lungs are able to move oxygen into the blood and remove carbon dioxide from the blood. ABG test An arterial blood gas (ABG) test is done to check for severe breathing problems and lung diseases, such as asthma, cystic fibrosis, or chronic obstructive pulmonary disease. PERSON: Tenille Johnson arterial blood gas test http://www.webmd.com/lung/arterial-blood-gases behavioral sensitization A material procesing technique where psychomotor stimulants are repeatedly administered, leading to the progressive augmentation of behavioral responses. This repeated administration produces gradual and incremental neuroadaptions that render the animals hypersensitive to these agents. Behavioral sensitization is used for alcoholics to induce reverse tolerance and help treat their addiction. PERSON: Tenille Johnson behavioral sensitization http://nba.uth.tmc.edu/homepage/dafny/neurobehav.html sound isolation enclosure An instrument that consists of an enclosed space that is used to reduce or isolate ambient and acoustic noise. PERSON: Tenille Johnson http://www.whisperroom.com/ isolation booth sound isolation enclosure patch clamp amplifier A patch clamp amplifier is a voltage amplifier that uses a single electrode clamp, where the voltage measuring and current passing circuits are connected. The electrode is attached to a wire that contacts the current/voltage loop inside the amplifier. Thus the electrode has only an indirect influence on the feedback circuit. The amplifier reads only the voltage at the top of the electrode, and feeds back current to compensate. A patch clamp amplifier is used to study action potentials in neurons. PERSON: Tenille Johnson http://en.wikipedia.org/wiki/Voltage_clamp#Single-electrode_voltage_clamp patch clamp amplifier electrolyte analyzer An analyzer for measuring the ionic values of electrolytes. Evaluation of electrolytes in a patient's blood. PERSON: Tenille Johnson electrolyte analyzer http://patft.uspto.gov/netacgi/nph-Parser?Sect2=PTO1&Sect2=HITOFF&p=1&u=%2Fnetahtml%2FPTO%2Fsearch-bool.html&r=1&f=G&l=50&d=PALL&RefSrch=yes&Query=PN%2F4705668 immunoperoxidase labeling HRP labeling of an antibody. Labeling of molecules with immunoperoxidase, a type of immunostain used in molecular biology, medical research, and clinical diagnostics. Immunoperoxidase reactions refer to a sub-class of immunohistochemical or immunocytochemical procedures in which the antibodies are visualized via a peroxidase-catalyzed reaction. PERSON: Karen Corday http://en.wikipedia.org/wiki/Immunoperoxidase time-of-flight secondary ion mass spectrometer A mass spectrometer that uses a target modified to achieve biochemical affinity with the analyte compound. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Surface-enhanced_laser_desorption/ionization nanodispenser A liquid handling device that is used for the pipetting and dispensing of volumes in the nanoliter range. PERSON: Erik Segerdell doi:10.1016/j.sna.2004.05.038 nanodispenser skin electrode An instrument that consists of a conductor through which an electric current enters or leaves the skin, whose electrical characteristics are being measured, used, or manipulated. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/electrode osmometer An instrument that measures the osmotic strength of a solution, colloid, or compound. PERSON: Tenille Johnson http://en.wikipedia.org/wiki/Osmometer osmometer cannulation A material processing technique where a tube is inserted into the body, often for the delivery or removal of fluid or for the gathering of data. Insertion of cannula Intubation of a patient to assist with breathing. PERSON: Nicole Vasilevsky cannulation http://en.wikipedia.org/wiki/Cannula electrophysiology data Data generated from an electrophysiology assay. Ion channel recording data from a primate suprachiasmatic nucleus. PERSON: Tenille Johnson PERSON: Tenille Johnson electrophysiology data technology transfer office An organization that provides services for commercialization and licensing of technologies at an institution. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Technology Transfer Office animal shocker A device that delivers a shock to an animal at programmable intervals. An animal shocker can be used in classical conditioning models. PERSON: Karen Corday Sacchetti, B., Sacco, T., & Strata, P. (2007). Reversible inactivation of amygdala and cerebellum but not perirhinal cortex impairs reactivated fear memories. European Journal of Neuroscience, 25(9), 2875-2884. DOI: 10.1111/j.1460-9568.2007.05508.x mineralized tissue preparation Histological sample preparation of biological materials that incorporate minerals into soft matrices to get the stiffness needed for a protective shield or structural support. PERSON: Karen Corday http://en.wikipedia.org/wiki/Mineralized_tissues animal physiology monitoring system A blood pressure monitoring system for mice. An instrument that is used to monitor mechanical, physical, or biochemical functions in an organism. PERSON: Erik Segerdell animal physiology monitor animal physiology monitoring system http://en.wikipedia.org/wiki/Physiology heart perfusion An organ perfusion technique of perfusing the heart by carrying fluid under pressure into the sectioned aorta and thus into the coronary system. Langendorff Heart Langendorff method PERSON: Tenille Johnson Perfusion of heart tissue with formaldehyde. http://www.medilexicon.com/medicaldictionary.php?t=54825 isolated perfused heart assay Prokaryota PERSON: Erik Segerdell Prokaryota The prokaryotes (pronounced /proʊˈkæri.oʊts/ or /proʊˈkæriəts/) are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles. http://en.wikipedia.org/wiki/Prokaryote plate luminometer A photometer used for measuring very low light levels (as those produced in a luminescent process) in a microplate format. PERSON: Karen Corday http://www.merriam-webster.com/medical/luminometer plate luminometer organic compound A chemical substance comprised of two or more elements combined, bonded in a fixed ratio and containing carbon and hydrogen atoms. The following elements can also be found in organic compounds: Nitrogen (N); oxygen (O), Fluor (F), phosphorous (P), sulfur (S), chlorine (Cl), selenium (Se), bromine (Br), iodine (I). Organic compounds do not contain metals. Benzene. PERSON: Edgar Miranda Placeholder for class to be imported from the Reagent Ontology (ReO). ; The definition of a compound requires a fixed ratio. Thus table salt, NaCl, is a compound but not a molecule, cecause it is composed of 2 or more elements in a fixed ratio (1:1, satisfying the definition of a compound) but does not have a well-defined number of atoms (so it does not meet the criteria for a molecule). It is instead an array of any number (not fixed) of Na+ and Cl- ions arranged in a 1:1 ratio. http://en.wikipedia.org/wiki/Chemical_compound organic compound bioinorganic compound A chemical comprised of 2 or more elements combined in a fixed ratio and containing metal, carbon, and hydrogen atoms. Hemoglobin is a bioinorganic compound. PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). ; The definition of a compound requires a fixed ratio. Thus table salt, NaCl, is a compound but not a molecule, cecause it is composed of 2 or more elements in a fixed ratio (1:1, satisfying the definition of a compound) but does not have a well-defined number of atoms (so it does not meet the criteria for a molecule). It is instead an array of any number (not fixed) of Na+ and Cl- ions arranged in a 1:1 ratio. bioinorganic compound http://en.wikipedia.org/wiki/Chemical_compound inorganic compound A chemical consisting of a well-defined number of atoms covalently bonded together, and containing metal atoms. Inorganic compounds do not contain chemical moities consisting of carbon and hydrogen bonded together. Examples of inorganic compounds are: Salts: sodium chloride (NaCl), magnesium sulfate (MgSO4), Oxides: carbon dioxide (CO2), silicon dioxide (SiO2) and Iron (II, III) oxide (Fe3O4), Acids: hydrogen chloride (HCl) and sulfuric acid (H2SO4), Bases: sodium hydroxide (NaOH). PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). ; The definition of a compound requires a fixed ratio. Thus table salt, NaCl, is a compound but not a molecule, cecause it is composed of 2 or more elements in a fixed ratio (1:1, satisfying the definition of a compound) but does not have a well-defined number of atoms (so it does not meet the criteria for a molecule). It is instead an array of any number (not fixed) of Na+ and Cl- ions arranged in a 1:1 ratio. Sodium chloride. http://en.wikipedia.org/wiki/Chemical_compound inorganic compound organic small molecule An organic small molecule is an organic molecule of low molecular weight, which is by definition not a polymer. The term small molecule is usually restricted to a molecule that also binds with high affinity to a biopolymer such as protein, nucleic acid, or polysaccharide and alters the activity or function of the biopolymer. The upper molecular weight limit for a small molecule is approximately 800 Daltons. PERSON: Melissa Haendel Phorbol 12-myristate 13-acetate is an organic small molecule that activates protein kinase C. Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/Small_molecule organic small molecule adeno-associated viruses AAV vectors have been used for clinical trials for treatment of cystic fibrosis. adeno-associated viruses baculoviral plasmid A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into baculoviral capsids for expression in target cells. Baculoviral expression systems are used for transient and stable protein expression in insect cells (and related invertebrates such as arachnids and crustaceans). PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://cshprotocols.cshlp.org/cgi/content/extract/2006/3/pdb.prot4512 retroviral plasmid A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into retroviral capsids for expression in target cells. DNA delivered by retroviral systems can be integrated into the host genome in a stable fashion in dividing cells. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/Viral_vector lentiviral plasmid A lentiviral plasmid expressing a gene of interest. A viral plasmid that is used to introduce genes into cells, which has the ability to integrate into the genome of non-dividing cells. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/Viral_vector adenoviral plasmid A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into adenoviral capsids for expression in target cells. DNA delivered by andenoviral systems does not integrate into the genome and is not replicated during cell division. The adenovirus is able to infect post-mitotic cells, making them especially useful for gene transfer into neuronal cells. An adenoviral plasmid expressing a gene of interest, used to study the function of the gene. PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). adenoviral plasmid http://en.wikipedia.org/wiki/Viral_vector research opportunity A planned process carried out by a person or organization with the objective of performing research. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Training grant to perform post-doctoral research. student research opportunity educational intervention An intervention which involves education, training programs, and courses in various fields and disciplines, and for training groups of persons. MeSH ID: Q000193 PERSON: Melanie Wilson PERSON: Melanie Wilson educational intervention dietary intervention An intervention that involves dietary and nutritional management. The concept does not include vitamin or mineral supplements, for which "drug intervention" may be used. MeSH qualifier id: Q000178. Definition excerpted from MeSH. PERSON: Melanie Wilson PERSON: Melanie Wilson To treat some illnesses or conditions, such as diabetes, a dietary intervention may be used. dietary intervention drug intervention A therapeutic intervention involving the administration of drugs, biologicals, chemicals, and antibiotics. Administration of a chemotherapy to treat cancer. MeSH ID: Q000188. Definition paraphrased from MeSH. PERSON: Melanie Wilson PERSON: Melanie Wilson drug intervention radiologic intervention An intervention that involves the therapeutic use of ionizing and nonionizing radiation. It includes the use of radioisotope therapy. MesH qualifier ID : Q000532 PERSON: Matthew Brush Radiation therapy for cancer. http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi radiologic intervention surgical intervention An intervention involving operative procedures on organs, regions, or tissues in the treatment of diseases, including tissue section by lasers. It excludes transplantation, for which "therapeutic intervention" is used. MeSH qualifier ID : Q000601 PERSON: Matthew Brush Surgical removal of a tumor. http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi surgical intervention rehabilitative intervention An intervention involving surgical procedures for restoration of function of the individual. MeSH qualifier ID : Q000534 PERSON: Matthew Brush http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi rehabilitative intervention nursing intervention An intervention involving nursing care and techniques in their management. It includes the nursing role in diagnostic, therapeutic, and preventive procedures. MeSH qualifier ID : Q000451 PERSON: Matthew Brush http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi nursing_intervention prevention and control intervention An intervention involving increasing human or animal resistance against disease (e.g., immunization), control of transmission agents, prevention and control of environmental hazards, or prevention and control of social factors leading to disease. It includes preventive measures in individual cases. MeSH qualifier ID : Q000517 PERSON: Matthew Brush http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi?mode=&index=218879&field=qual&HM=&II=&PA=&form=&input= prevention and control intervention psychological and behavioral intervention PERSON: Matthew Brush PERSON: Melanie Wilson Psychological or behavior intervention is a combination of program elements, strategies, or modalities designed to influence psychological or behavioral processes or outcomes. psychological and behavioral intervention x-ray crystallography assay A molecular assay used to determine the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and diffracts into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their disorder and various other information. PERSON: Karen Corday X ray crystallography assay Xray Crystallography http://en.wikipedia.org/wiki/X-ray_crystallography genome assembly A data analysis technique taking a large number of short DNA sequences, generated by DNA sequencing, and putting them back together to create a representation of the original chromosomes from which the DNA originated. PERSON: Karen Corday http://en.wikipedia.org/wiki/Genome_project Raman confocal microscope A confocal microscope that consists of of an optical microscope, an excitation laser, a monochromator, and a sensitive detector (such as a charge-coupled device or photomultiplier tube), has high spatial resolution, and relies on inelastic scattering, or Raman scattering, of monochromatic light. PERSON: Melanie Wilson Raman confocal microscope Raman microscope Used to image biological samples. http://en.wikipedia.org/wiki/Raman_spectroscopy SNP data Data that describes single nucleotide polymorphisms, or SNPs (pronounced "snips"), which are DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered. PERSON: Matthew Brush SNP data http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml fluorescence recovery after photobleaching An imaging assay that allows determination of the kinetics of diffusion in living cells (usually) using fluorescence microscopy. The general method is to label a specific cell component with a fluorescent molecule, image that cell, photobleach a small portion of the cell, then image the recovery of fluorescence over time. Can be used to study cell membrane diffusion. FRAP Fluorescence photobleaching recovery PERSON: Nicole Vasilevsky http://microscopy.berkeley.edu/courses/tlm/fluor_techniques/FRAP.html field emission scanning electron microscope A scanning electron microscope that has electromagnetic coils that form an electron beam that scans the object (scan) and secondary electrons are produced by interaction with the atoms at the surface of the sample. Can be used to image biomolecules. FESEM PERSON: Karen Corday http://www.vcbio.science.ru.nl/en/fesem/ measurement instrument A pH meter is used to measure the pH of a sample. An instrument that has 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. OBI PERSON: Nicole Vasilevsky image acquisition instrument A microscope. An instrument that has image acquisition function. An image acquisition function is a function to acquire an image of a material. OBI PERSON: Nicole Vasilevsky viral plasmid A pWPI-Mad4-GFP vector. A plasmid carrying sequence elements that allow for packaging of genetic cargo into viral capsids, DNA replication, and expression in target cells. Viral plasmids may contain additional genes required for capsid protein production and assembly, or may require helper plasmids which produce these proteins. PERSON: Matthew Brush PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). adeno-associated viral plasmid A viral plasmid carrying sequence elements that allow for packaging of genetic cargo into baculoviral capsids for expression in target cells. Adeno-associated viral expression systems can be used with non-dividing cells, and cargo DNA has the ability to stably integrate into the host cell genome at a specific site (designated AAVS1) in the human chromosome 19. AAV plasmid An adeno-associated viral plasmid expressing a gene of interest, used to study the function of the gene. PERSON: Matt Brush. By David P. Clark, Nanette Jean Pazdernik PERSON: Nicole Vasilevsky Placeholder for class to be imported from the Reagent Ontology (ReO). prokaryotic expression construct An expression construct that contains promoter elements to drive expression of downstream genes in prokaryotic cells or prokaryote-derived in vitro expression systems. PERSON: Matthew Brush PERSON: Matthew Brush Placeholder for class to be imported from the Reagent Ontology (ReO). center An organization where a particular activity or service is concentrated. Center for Environmental and Toxicological Research. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/center true information processing instrument A computer. An instrument that has 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. OBI PERSON: Nicole Vasilevsky material separation instrument A chromatography column. An instrument that has material separation function. A material separation function is a function that increases the resolution between two or more material entities. The distinction between the entities is usually based on some associated physical quality. OBI PERSON: Nicole Vasilevsky sterilization instrument An autoclave. An instrument that has sterilization function. Sterilization function is a function to remove viable organisms from an input material. OBI PERSON: Nicole Vasilevsky mechanical instrument A drill is a mechanical instrument. An instrument that has mechanical function. A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). OBI PERSON: Nicole Vasilevsky environment control instrument A laminar flow hood. An instrument that has 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. OBI PERSON: Nicole Vasilevsky material transfer instrument An automatic coverslipper. An instrument that has transfer function. A transfer function is a function to displace a material from one location to another. OBI PERSON: Nicole Vasilevsky nucleic acid reagent A primer. PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). Reagent that is a polymer comprised of nucleotides, each of which consists of three components: a nitrogenous heterocyclic base, which is either a purine or a pyrimidine; a pentose sugar; and a phosphate group. http://en.wikipedia.org/wiki/Nucleic_acid primer Nucleic acid reagent that is a short strand of nucleic acid that serves as a starting point for DNA or RNA synthesis. Oligos used in PCR. PERSON: Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29 morpholino Morpholinos are injected into zebrafish to study a particular gene's function. Nucleic acid reagent that is a short strand of nucleic acid where the bases are bound to morpholine rings instead of deoxyribose rings and linked through phosphorodiamidate groups instead of phosphates. Morpholinos are used to knockdown gene expression via antisense binding. PERSON:Melissa Haendel Placeholder for class to be imported from the Reagent Ontology (ReO). http://en.wikipedia.org/wiki/Morpholino spore trap An instrument designed to capture and quantify a broad spectrum of fungal spores present in the air. PERSON: Nicole Vasilevsky http://www.emlab.com/s/sampling/SporetrapSampling.html calcium imaging assay Ca imaging Ca2+ imaging assay An imaging assay that is designed to show the calcium (Ca2+) levels of a tissue or medium. Ca imaging assay Ca2+ imaging Can be used to assay calcium levels in muscle cells. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Calcium_imaging apoptotic DNA ladder assay An apoptosis assay that allows for detection of DNA fragmentation in apoptotic cells. DNA fragments can be visualized by agarose gel electrophoresis. An apoptotic DNA ladder assay can be used to determine if cells are undergoing apoptosis after treatment with a cytolytic drug. PERSON: Nicole Vasilevsky http://www.abcam.com/Apoptotic-DNA-Ladder-Detection-Kit-ab66090.html cell proliferation assay A cellular assay that allows for the measurement of the multiplication or reproduction of cells, resulting in the expansion of a cell population. Cell division assay OBI PERSON: Nicole Vasilevsky Tritiated thymidine incorporation. multiplex bead assay A molecular assay that permits the simultaneous measurement of an array of proteins in a single, small volume sample. Elshal and McCoy (2006) Methods. 38(4): 317–323. Multiplex assay PERSON: Nicole Vasilevsky picogreen assay An assay used for DNA quantificiation. An biomolecular label detection assay used for quantification of double-stranded DNA (dsDNA) in molecular biology assays. PERSON: Nicole Vasilevsky http://www.topac.com/picogreen.html cycle sequencing A DNA sequencing by synthesis technique used to increase the sensitivity of the DNA sequencing process and permits the use of very small amounts of DNA starting material. This is accomplished by using a temperature cycling process similar to that employed in the polymerase chain reaction. PERSON: Nicole Vasilevsky Sequencing of a genome. http://www.answers.com/topic/cycle-sequencing injection Agent delivery whereby a substance is introduced into a organism, usually by means of a hypodermic syringe, as a liquid into the veins or muscles of the body. Injection of a drug. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/injection intracytoplasmic sperm injection DISCO Direct injection of sperm into cytoplasm of the oocyte ICSI Injection of a single sperm into a single celled embryo or an egg for the purpose of in vitro fertilization. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Intracytoplasmic_sperm_injection administration of inhalational agents Administration of anesthesia to mice. Agent delivery performed to humanely administer inhalation agents to organism, usually for the purpose of sedation. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky agent delivery A material processing technique performed to locally deliver an agent to a recipient. An injection. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky RNA quality analysis A nucleic acid assay used to determine quality of RNA after purification for the purpose of downstream molecular assays. RNA quality can be checked by electrophoresis in agarose gel, by electrophoresis in polyacrylamide gel, or by in vitro translation. PERSON: Nicole Vasilevsky RNA QA Spectrophotometric analysis of RNA after purification from a sample. http://www.molecularinfo.com/MTM/C/C3/C3-5/C3-5-5.html amino acid isolation Amino acid purification PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Sample preparation for assay that involves the isolation of amino acids from a cell or tissue sample for use in protein chemistry or biological assays. The collection of adenine from a sample of blood plasma is amino acid isolation. quantitative southern blot analysis A Southern blot analysis technique performed to quantitate the bands on a Southern blot to compare the relative expression levels of a particular gene. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky DNA purification Nucleic acid purification of genomic or plasmid DNA from other impurities, such as bacteria or contaminating materials for the purpose of molecular biology research. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Purification of a plasmid from a bacterial culture. in vivo reproductive system test A physiological assay that tests the reproductive system function in the whole, living organism for research purposes. Clinical monitoring of the menstrual cycle. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky transverse aortic constriction A surgical procedure performed to stress the heart, which causes a subacute increase in the workload on the heart, which is a commonly used surgical model of cardiac hypertrophy and subsequent failure. Arany et al (2006) PNAS 103:10086. Can be used to study stroke. PERSON: Nicole Vasilevsky cryoablation A material processing technique that uses extreme cold (cryo) to remove tissue (ablation). Cryocautery Cryodestruction Cryosurgery PERSON: Nicole Vasilevsky Warts are removed by cryoablation. http://en.wikipedia.org/wiki/Cryoablation in vivo bioluminescence An imaging assay that allows detection of bioluminescence from a living organism or organisms. Detection of GFP in a sample. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky radioimmunoassay A RAST test (radioallergosorbent test) is an example of radioimmunoassay. A radioactivity detection technique that uses the binding of a radioactively labeled substances to an antibody in order to analyze minute amounts of proteins in a sample. PERSON: Nicole Vasilevsky RIA http://en.wiktionary.org/wiki/radioimmunoassay protein quantitation assay A protein assay used for determination of protein concentrations in solutions that depends upon the change in absorbance of a colored substrate upon binding of protein. BCA assay Bradford assay. PERSON: Nicole Vasilevsky biuret assay bradford assay http://www.animal.ufl.edu/hansen/protocols/minibradford.htm lowry assay protein concentration assay tissue co-culturing Culturing two cell types together. OBI branch derived PERSON: Nicole Vasilevsky Tissue culture of two or more different types are are combined and allowed to culture as one. DNA quality analysis A nucleic acid assay used to determine quality of DNA after purification for molecular biology research. Assays to determine DNA quality include DNA electrophoresis and spectrophotometric determination of the ratio of the A260/A280. DNA QA PERSON: Nicole Vasilevsky Spectrophotometric analysis of DNA after purification from a sample. www.generationcp.org/capcorner/gcp_training.../practicals_3.doc identification of differentiated hematopoietic stem cells A cellular assay used to identify the process by which a hematopoietic stem cell (HSC) becomes a more specialized cell. HSCs are multipotent stem cells that give rise to all the blood cell types including myeloid (monocytes and macrophages, neutrophils, basophils, eosinophils, erythrocytes, megakaryocytes/platelets, dendritic cells), and lymphoid lineages (T cells, B cells, NK cells). PERSON: Nicole Vasilevsky Use of flow cytometry to identify differentiation stem cells from undifferentiated cells. http://en.wikipedia.org/wiki/Hematopoietic_stem_cell metagenomics analysis A molecular assay that is used to analyze metagenomic data; genetic material recovered directly from environmental samples for genomic research. PERSON: Nicole Vasilevsky community genomic analysis ecogenomic analysis environmental genomic analysis http://en.wikipedia.org/wiki/Metagenomics pathway data analysis A data analysis technique that allows for analysis of data relating to biological pathways accumulated from genomic, proteomic or other sources. Analysis of cell signaling data. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky clinical monitoring A clinical assay that involves oversight and administrative efforts that monitor a participant's health during a clinical trial. Monitoring a patient in a clinical trial. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Clinical_monitoring in utero electroporation Electroporation into the uterus or ovaries of an organism to overexpress a protein of interest. PERSON: Nicole Vasilevsky Shimogori and Ogawa (2008) Develop. Growth Differ. 50, 499–506 Transfection of a protein into the uterus. in utero transfrection in ovo electroporation Electroporation into chick embryos to overexpress a protein of interest. PERSON: Nicole Vasilevsky Transfection of a plasmid into chick embryos. http://www.cellscience.com/reviews1/Ovarian_Transplantation_and_Cryopreservation.html in ovo transfection ovarian transplantation PERSON: Nicole Vasilevsky Transplantation of ovaries into an organism, often performed for women who have lost their fertility due to medical treatment, disease or aging. http://www.cellscience.com/reviews1/Ovarian_Transplantation_and_Cryopreservation.html in vitro follicle maturation Culture and maturation of ovarian follicles in vitro for clinical applications. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/In_vitro_maturation ovarian radiation Irridiation of ovaries, usually for the purpose of cancer treatment. PERSON: Nicole Vasilevsky http://www.oncologychannel.com/ovariancancer/radiotherapy.shtml ovarian radiotherapy mutant strain generation PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Production of transgenic mice. Specimen creation of mutant strain of cells or an organism for the purpose of studying gene function. multi-spectral fluorescence An imaging assay that uses the synergistic combination of imaging and spectroscopy with broad applications in both preclinical and clinical settings. Imaging of tumor cells in a rodent model that are labels with fluorophores, such as GFP. PERSON: Nicole Vasilevsky Zhou and El-Deiry (2009) Journal of Nuclear Medicine 50:1563-1566 virus neutralization A material processing technique used for detection of virus-specific neutralizing antibodies in a sample. PERSON: Nicole Vasilevsky Virus attenuation Zielinska etl a (2005) Virology Journal 2005, 2:84. tenocyte differentiation screening A cellular assay used to screen culture skin-derived tenocyte cells for the proper phenotype for research and clinical applications with tendon tissue. PERSON: Nicole Vasilevsky Schulze-Tanzil (2004) 122:219-228 serology assay A tissue/organ assay that is performed to analyze blood serum and other bodily fluids, to identify antibodies in the serum. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Serology calorimetry A molecular assay that is used to measure the heat of chemical reactions or physical changes. An assay to measure the volume of oxygen consumption and volume of carbon dioxide output in a patient. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Calorimetry track breeding pairs A mouse breeding technique to track parental breeders to generate offspring in an animal colony. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Used for development of transgenic mice strains. reactive oxygen species assay A molecular assay used to detect the presence of reactive oxygen species on a molecule, to determine if they play a role in physiological or pathophysiological processes. An assay to detect NOS in a sample. Dikalov et al (2007) Hypertension 49:717-727. PERSON: Nicole Vasilevsky ROS assay experimental glucuronidation Chemical modification of a molecule in an experimental setting, to increase the water solubility by adding glucuronic acid. PERSON: Marc Le Pape PERSON: Nicole Vasilevsky tissue fixation Fixation of biological tissues to preserve them from decay, either through autolysis or putrefaction. Fixation terminates any ongoing biochemical reactions, and may also increase the mechanical strength or stability of the treated tissues. Fixation is usually the first stage in a multistep process to prepare a sample of biological material for microscopy or other analysis Fixing tissue prior to immunohistochemistry staining. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Fixation_%28histology%29 in vivo electrophysiology recording An electrophysiology assay that measures voltage changes or electric currents in single ion channel proteins to whole organs. In neuroscience, it includes measurements of the electrical activity of neurons, and in particular, action potential activity. EKG is a common method for electrophysiology recording. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Electrophysiology transcranial magnetic stimulation A material processing technique used to cause depolarization in the neurons of the brain. TMS uses electromagnetic induction to induce weak electric currents using a rapidly changing magnetic field; this can cause activity in specific or general parts of the brain, allowing the functioning and interconnections of the brain to be studied. PERSON: Nicole Vasilevsky TMS http://en.wikipedia.org/wiki/Transcranial_magnetic_stimulation mitochondrial oxygen consumption measurement A cellular assay used to measure oxygen consumption in mitochondria to study mitochondrial respiration, which can be used to diagnosis mitochondrial disorders. Jonckheere et al (2010) Clinical Chemistry 56:424-431. PERSON: Nicole Vasilevsky mitochondrial permeability transition measurement A cellular assay used to measure membrane potential and permeability transition in the mitochondria during apoptosis. Mitochondrial membrane permeabilization constitutes an early event of the apoptotic process (programmed cell death). PERSON: Nicole Vasilevsky Zamzami and Kroemer (2004) Methods in Molecular Biology 282:103-115. measurement of mitochondrial membrane potential A cellular assay used to measure mitochondrial membrane potential for the assessment of mitochondrial function. PERSON: Nicole Vasilevsky http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-60761-411-1_7 fast live imaging An imaging assay that involves live imaging of cells, that enables subsecond, multicolor four-dimensional data acquisition, which has the unique capability to probe dynamic processes, linking molecular components and their localization with function. Carlton et al (2010) 107:16016-16022 Imaging of in vivo biological processes in a cell. Live cell imaging PERSON: Nicole Vasilevsky Time-lapse imaging Time-lapse microscopy morphological changes assay A cellular assay that is performed to analyze changes in the form and structure of organisms and their specific structural features. Can be used to detect apoptotic cells, which undergo morphological changes. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Morphology_%28biology%29 caspase assay An apoptosis assay used to measure caspase activity, which are proteases that mediate apoptosis. Analysis of caspase activity by flow cytometry. PERSON: Nicole Vasilevsky http://www.answers.com/topic/caspase-2 annexin V assay An apoptosis assay used to detect apoptosis at a very early stage. This assay takes advantage of the fact that phosphatidylserine (PS; 1–3) is translocated from the inner (cytoplasmic) leaflet of the plasma membrane to the outer (cell surface) leaflet soon after the induction of apoptosis, and that the annexin V protein has a strong, specific affinity for PS (4–6). PS on the outer leaflet is available to bind labeled annexin V, providing the basis for a simple staining assay. Cells undergoing apoptosis can be detected by Annexin V staining. PERSON: Nicole Vasilevsky http://www.clontech.com/products/detail.asp?product_id=10378&tabno=2 in vitro cytotoxicity assay An assay used to investigate the function of NK cells. An cellular assay that measures basal cytotoxicity (general cytotoxicity that affects structures or processes intrinsic to all cell types) in response to external insults. Cytotoxicity assay PERSON: Nicole Vasilevsky http://iccvam.niehs.nih.gov/methods/acutetox/acutetox.htm clinical laboratory results management A data management technique that specifies how to manage data from clinical laboratory studies, such as chemical, microscopic and bacteriologic tests of blood, tissue and fluids. PERSON: Nicole Vasilevsky http://medical-dictionary.thefreedictionary.com/clinical+laboratory+scientist blood sampling Blood drawing for cholesterol screening. Collection of a blood specimen from an organism, usually performed by a closed method, either a hypodermic syringe or a vacuumized container, usually for the purpose of laboratory examination. PERSON: Nicole Vasilevsky http://medical-dictionary.thefreedictionary.com/blood+sampling medicine storage Material storage of medication in a health care setting that allows access to only authorized personel. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky research subject private information management A clinical trial technique that maintains privacy of patient health records, who are participating as research subjects to protect them from unwarranted invasions of personal privacy. PERSON: Nicole Vasilevsky Protection of private patient information in a clinical trial. http://www.epa.gov/privacy/index.htm; http://en.wikipedia.org/wiki/Human_subject_research research subject consent A clinical trial technique used to educate potential subjects to ensure that they can reach a truly informed decision about whether or not to participate in the research. Their consent must be given freely, without coercion and must be based on a clear understanding of what participation involves. Consent to participate in a clinical trial. PERSON: Nicole Vasilevsky http://healthcare.partners.org/phsirb/infcons.htm informed consent of research subjects array scanning A molecular assay used for scanning a surface, consisting of focusing an array of optical beams using optics having an axis, so as to illuminate a region of the surface intercepted by the axis, such that each optical beam illuminates a portion of a respective sub-region within the region. PERSON: Nicole Vasilevsky http://www.freshpatents.com/Optical-spot-grid-array-scanning-system-dt20070614ptan20070133077.php array printing A material processing technique that involves printing samples onto a solid substrate to allow researchers to efficiently screen thousands of conditions in a very small space for applications in drug screening, molecular biology, and genetic analysis. Array spotting PERSON: Nicole Vasilevsky Screening potential new drug targets. http://aurorabiomed.com/app_peptide.htm high throughput sample analysis An assay that allows for high throughput analysis of samples. High throughput screening Next generation sequencing. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky nucleic acid shearing A material processing technique used to fragment DNA molecules by mechanical force. DNA shearing PERSON: Nicole Vasilevsky Passing DNA through a needle shears the DNA. http://www.mondofacto.com/facts/dictionary?DNA+shearing SNP interrogation genotyping A genotyping technique that interrogates SNPs by hybridizing complementary DNA probes to the SNP site. DNA sequence variation genotyping PERSON: Nicole Vasilevsky SNP analysis SNP chip analysis SNP genotyping SNP sampling Single nucleotide polymorphism analysis Single nucleotide polymorphism gentotyping Single nucleotide polymorphism sampling http://en.wikipedia.org/wiki/SNP_genotyping oocyte injection Brown and Corbin (2002) Methods in Molecular Biology 180:39-70. Injection of materials into oocytes, the female gametocyte or germ cell involved in reproduction, of an organism for the purpose of generating transgenic offpsring. PERSON: Nicole Vasilevsky Transgenic mouse generation. telemetric blood pressure monitoring procedure A physiological assay that is used to directly measure blood pressure via an implantable radio telemetry device in an organism, used to study hypertension. Huetteman and Bogie (2009) Methods Mol Biol. 573:57-73. PERSON: Nicole Vasilevsky in vitro fertilization A culture and propogation technique performed in vitro to the fuse of gametes to produce a new organism. IVF PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Fertilisation non-web programming A technique that involves creating a computer program that is non-web based. It involves developing the program logic to solve the particular problem, writing the program logic in a specific programming language (coding the program), assembling or compiling the program to turn it into machine language, and testing and debugging the program. PERSON: Nicole Vasilevsky Writing a program in JAVA that can sort numbers. http://www.pcmag.com/encyclopedia_term/0%2C2542%2Ct%3Dprogramming&i%3D49827%2C00.asp biological sample processing A material processing technique that involves the careful handling and storage of precious biological samples with the goal of obtaining a large amount of information from limited samples for cytogenetic, immunological, biochemical or other analyses. Holland et al (2003) Mutation Research/Reviews in Mutation Research, Volume 543: 217-234 PERSON: Nicole Vasilevsky Purification of DNA from a sample, for subsequent sequence analysis. polyclonal antibody production Antibody production of polyclonal antibodies by immunization of a suitable mammal, such as a mouse, rabbit or goat. An antigen is injected into the mammal. This induces the B-lymphocytes to produce IgG immunoglobulins specific for the antigen. This polyclonal immunoglobulin is purified from the mammal's serum. PERSON: Nicole Vasilevsky Polyclonal IgG preparation Production of a rabbit anti-human OX40 antibody. http://en.wikipedia.org/wiki/Polyclonal_antibodies plasmid purification A purification technique used to extract and purify plasmid DNA. It involves growing bacterial cultures that express the plasmid, harvesting and lysing the bacteria and purifying the plasmid DNA. PERSON: Nicole Vasilevsky Purification of a plasmid from a bacterial culture. http://en.wikipedia.org/wiki/Plasmid_preparation label free mass spectrometry A mass spectrometry assay that allows for measurement for endogenous targets in live cell assays, and eliminates the need for tags, dyes, or specialized reagents or engineered cells. Label free relative quantitative analysis PERSON: Nicole Vasilevsky http://www.moleculardevices.com/Products/Instruments/Label-Free-Analysis.html?gclid=CMTUq7Gi3aQCFQsGbAodNhAjKg multiple reaction monitoring analysis by mass spectrometry A mass spectrometry based assay, based on multiple reaction monitoring of stable isotope-labeled peptides, that enables highly reproducible quantification of hundreds of nodes (phosphorylation sites) within a signaling network and across multiple conditions simultaneously. MRM PERSON: Nicole Vasilevsky Wolf-Yadlin et al (2007) PNAS 104:5860-5865 post translational modification identification by mass spectrometry A mass spectrometry assay that identifies post translational modifications to proteins in a sample. Identification of phosphorylated residues on a protein. PERSON: Nicole Vasilevsky http://www.ohsu.edu/xd/research/research-cores/proteomics/request-services/index.cfm post translational modification localization by mass spectrometry A mass spectrometry assay used to identify the location and mass shift of the modification on a protein. Identification of phosphorylated residues on a protein. PERSON: Nicole Vasilevsky http://www.ohsu.edu/xd/research/research-cores/proteomics/request-services/index.cfm protein mass determination by mass spectrometry A mass spectrometry assay used to determine the molecular weight of a given protein. Determination of molecular weight of a protein. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Protein mass analysis partial protein sequencing A protein sequencing assay used to partially sequence the protein to determine the order of amino acids in protein sequences to identify an unknown protein, typically done by mass spectrometry. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Partial protein sequencing of a purified can be used to confirm the identify of an unknown protein. human subject recruitment and protection A clinical trial technique used to recruit human subjects for clinical trials and to protect their privacy. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Recruiting patients for a clinical trial to investigate the usage of a new drug and protecting their privacy. risk management A technique used for identification, assessment, and prioritization of risks followed by coordinated and economical application of resources to minimize, monitor, and control the probability and/or impact of unfortunate events or to maximize the realization of opportunities. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Risk_management autoradiography A radioactivity detection technique using X- ray film to visualize molecules or fragments of molecules that have been radioactively labeled. Autoradiography has many applications in the laboratory. Detection of radiolabeled proteins in a pulse-chase assay. PERSON: Nicole Vasilevsky Radioautography http://www.medterms.com/script/main/art.asp?articlekey=2405 sample irradiation Irradiation of samples or the condition of samples being exposed to radition. Can be performed for sterilization or for immune suppression. Irradiation of splenocytes in vitro. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/irradiation rodent irradiation Irradiation of mice, prior to bone marrow transplant. Irradiation of rodents or the condition of rodents being exposed to radiation. Accurate partial or whole body irradiation can be used for many types of investigations, including tumor studies and experiments studying the immune response. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/irradiation, Woo and Nordal (2006) Biomed Imaging Interv J 2:e10. bone marrow analysis A tissue/organ assay performed to analyze cells in the bone marrow, such as red blood cells, white blood cells, or platelets for research or diagnostic purposes. Analysis of the white blood cell count. PERSON: Nicole Vasilevsky http://www.webmd.com/cancer/bone-marrow-aspiration-and-biopsy fluorescence activated cell sorting (FACS) A flow cytometry assay that provides a method for sorting a heterogeneous mixture of biological cells into two or more containers, one cell at a time, based upon the specific light scattering and fluorescent characteristics of each cell. FACS PERSON: Nicole Vasilevsky Sorting of specific cell populations, such as CD4+ T cells. http://en.wikipedia.org/wiki/Flow_cytometry data entry A data transformation technique that involves transcribing some form of data into another form, usually a computer program. Entry of data about research resources into eagle-i. PERSON: Nicole Vasilevsky http://www.wisegeek.com/what-is-data-entry.htm patient screening A clinical assay that is performed as a preliminary procedure, such as a test or examination, to detect the most characteristic sign or signs of a disorder or a condition that may require further investigation. PERSON: Nicole Vasilevsky Patients are screened during the recruitment process of a clinical trial, to ensure they meet the criteria. http://medical-dictionary.thefreedictionary.com/screening immunogold labeling Labeling of antibodies with collodial gold particles. Labeling of of proteins, antigens, and other macromolecules of interest with colloidal gold particles, which are most often attached to secondary antibodies which are in turn attached to primary antibodies designed to bind a specific protein or other cell component. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Immunogold_labelling antigen capture and purification A material component separation technique used in the isolation of antigens from complex mixtures. Desai and Dworecki (2004) Anal Biochem. 328(2):162-5. Isolation of solubilized proteins from a sample. PERSON: Nicole Vasilevsky cell separation A material component separation technique used to separate populations of two or more cells, such as by magnetic bead sorting. Cell isolation Cell purification Cell segregation Cell sorting PERSON: Nicole Vasilevsky Separation and isolation of CD4 T cells. http://www.reference.md/files/D002/mD002469.html drug binding assay A molecular assay used to assay the binding of a drug to a large molecule in tissues or fluids, e.g. binding to protein in the blood, may affect the metabolism of the drug, especially its rate of excretion. Assay to determine if a monoclonal antibody drug is reaching it's intended target receptor. PERSON: Nicole Vasilevsky http://medical-dictionary.thefreedictionary.com/drug+binding lipotoxicity assay A tissue/organ assay used to assay the fatty acid accumulation in non-adipose tissues. An assay to analyze pancreatic Î_-Cell function. PERSON: Nicole Vasilevsky Schaffer (2003) Curr Opin Lipidol. 14(3):281-287. riboprobe production Material production of RNA probes that can be produced by in vitro transcription of cloned DNA inserted in a suitable plasmid downstream of a viral promoter for the purpose of producing sense and antisense riboprobes. PERSON: Nicole Vasilevsky Production of riboprobes for in situ hybridization. http://en.wikipedia.org/wiki/Riboprobe viral infection Experimental infection using viruses or viral products to introduce a gene product into in vitro systems or animal models. Infecting cells with viral supernatants. PERSON: Nicole Vasilevsky Transduction http://en.wikipedia.org/wiki/Lentivirus nucleic acid amplification Enzymatic amplification of specific nucleic acids to levels where they can be detected in downstream applications. Examples are PCR, TMA, NASBA, etc. PERSON: Nicole Vasilevsky Polymerase chain reaction. http://groups.molbiosci.northwestern.edu/holmgren/Glossary/Definitions/Def-N/nucleic_acid_ampl_assay.html TUNEL labeling A labeling method used for detecting the 3'-OH ends of DNA exposed during the internucleosomal cleavage that occurs during apoptosis. Incorporation of biotinylated dUTP allows detection by immunohistochemical procedures. The labeled apoptotic cells may be visualized by light microscopy. An assay used to detect apoptotic cells. PERSON: Nicole Vasilevsky TUNEL staining http://www.scienceboard.net/resources/protocols.asp?action=article&protocol_id=41&criteria= terminal deoxynucleotidyl transferase mediated dUTP-biotin nick end labeling small animal surgery Induction of stroke in an animal model. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Surgical procedures on small animals for research purposes. coronary artery ligation A surgical procedure that involves ligation of the coronary artery in the heart, which is used in in vivo animal models to study myocardial infarction. Induction of a stroke in an animal model. Ligation of anomalous coronary artery PERSON: Nicole Vasilevsky Ye et al (1997) Molecular and Cellular Biochemistry. 176:227-233. left anterior descending artery ligation Coronary artery ligation of the left anterior descending artery, which is performed to induce left ventricular infarction for research purposes. PERSON: Nicole Vasilevsky Samsamshariat, Samsamshariat and Movahed (2005) Cardiovasc Revasc Med. 6:121 Used for stroke models. spinal cord laminectomy A spinal cord laminectomy can be performed to relieve pain after injury. A surgical procedure that involves surgical removal of the portion of the vertebral bone called the lamina, which is designed to relieve pressure on the spinal cord (or nerve) from herniated discs, spinal stenosis and other related conditions. PERSON: Nicole Vasilevsky http://www.articlesbase.com/diseases-and-conditions-articles/lumbar-laminectomy-a-surgery-on-spinal-cord-1237643.html spinal decompression lentivirus production PERSON: Nicole Vasilevsky Production of high-titers of lentivirus expressing a gene of interest, to study the function of that gene. Virus production of high-titer, lentivirus prepartions for use in gene delivery applications. http://web.mit.edu/jacks-lab/protocols/lentiviralproduction.htm tissue digestion A material processing technique that is used to digest human, animal or plant tissue by dissolving the remains by alkaline hydrolysis or other methods for the purpose of disposal of the remains or subsequent analysis of components of the tissue. PERSON: Nicole Vasilevsky Tissue from mice is digested prior to genotyping, to isolate the DNA. http://www.wisegeek.com/what-is-tissue-digestion.htm site-directed mutagenesis A material processing technique in which a mutation is created at a defined site in a DNA molecule for research purposes. Oligonucleotide directed mutagenesis Oligonucleotide-directed mutagenesis PERSON: Nicole Vasilevsky Site specific mutagenesis Site-directed mutagenesis can be used to alter the function of a protein, such as make the avian flu virus transferrable to other species. Site-specific mutagenesis http://en.wikipedia.org/wiki/Site-directed_mutagenesis bioinformatics analysis A data transformation technique that involves the analysis of bioinformatics data, which is the application of statistics and computer science to the field of molecular biology. Analysis of DNA sequence data. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Bioinformatics research electronic datacapture A technique designed for the collection of clinical data in electronic format for use mainly in human clinical trials. Electronic health records. PERSON: Nicole Vasilevsky clinical database development http://en.wikipedia.org/wiki/Electronic_data_capture web programming A technique that involves writing the necessary source code to create a Web site. It refers to writing the HTML pages or JavaScript in the pages, and any Web site that provides searches, access to databases or any custom processing for the user requires additional programs that run in the Web server. Web server processing is programmed in Java, VBScript, Perl and other languages. Creation of a website. PERSON: Nicole Vasilevsky Web development http://www.pcmag.com/encyclopedia_term/0,2542,t=Web+programming&i=54332,00.asp analog electronics design An instrument and electronics design technique that involves the design of analog electronics; electronic systems with a continuously variable signal. Design of an analog instrument, used to measure current. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Analogue_electronics circuit board layout design An instrument and electronics design technique that involves the design of printed circuit boards; a component made of one or more layers of insulating materials with electrical conductors, which is used in computers. PERSON: Nicole Vasilevsky http://www.smps.us/pcb-design.html electronic instrument design An instrument and electronics design technique that involves the design, prototyping, rework, final engineering, and documentation of electronic instruments. Design of a flow cytometer. PERSON: Nicole Vasilevsky http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=3694 gene expression analysis assay A molecular assay used to analyze the location or quantity of of gene expression. DNA expression analysis Gene expression pattern analysis Gene expression profiling PERSON: Melissa Haendel PERSON: Nicole Vasilevsky Real-time PCR is performed to detect relative gene expression in a sample. Transcript expression analysis Instrumentation fabrication Fabrication of a robot. Manufacturing of a flow cytometer. Manufacturing of an instrument from raw materials. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/fabrication instrumentation planning An instrument and electronics design technique that involves planning of instrumentation design and fabrication. Equipment design and fabrication service provided by a lab. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky optical system design A instrument and electronics design technique that involves the design, layout and analysis of various optical systems; from single element designs to complex wide angle imaging system designs. Design of a microscope. PERSON: Nicole Vasilevsky http://www.loganopticaldesign.com/ protein interaction detection A protein assay used to detect protein-molecule interactions, a biological process of proteins binding to cellular molecules, such as DNA, often to carry out their biological function such as gene expression. Co-immunoprecipitation is used to detect protein-protein interaction. PERSON: Nicole Vasilevsky Protein binding assay http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction protein-DNA interaction detection Gel mobility shift assay to detect proteins that bind to specific DNA elements. PERSON: Nicole Vasilevsky Protein interaction detection technique used to analyze specific protein-DNA interactions, including DNase I footprinting, gel mobility shift assay, nitrocellulose filter binding assay, genetic analysis or x-ray crystallography for the purpose of studying gene expression or regulation. Protein-DNA binding assay http://www.biochem.arizona.edu/classes/bioc568/protein_dna_interactions.htm skeletal morphogenesis analysis An organismal assay that is performed to analyze the formation of a skeleton or skeletal elements at various developmental stages in an organism. Limb development can be studied by analyzing skeletal morphogenesis. PERSON: Nicole Vasilevsky http://www.springerprotocols.com/Abstract/doi/10.1385/1-59259-065-9:61 printed circuit board design An instrument and electronics design technique used to design printed circuit boards, which are used to mechanically support and electrically connect electronic components using conductive pathways, tracks or signal traces etched from copper sheets laminated onto a non-conductive substrate. It is also referred to as printed wiring board (PWB) or etched wiring board. PCB design PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Printed_circuit_board video over IP A technique that uses an existing standard video codec to reduce the program material to a bitstream (e.g., an MPEG transport stream), and then to use an Internet Protocol (IP) network to carry that bitstream encapsulated in a stream of IP packets. PERSON: Nicole Vasilevsky Professional video over IP Skype. http://en.wikipedia.org/wiki/Professional_video_over_IP streaming media delivery method A technique that involves streaming multimedia that are constantly received by, and normally presented to, an end-user while being delivered by a streaming provider (including audio or video playback). PERSON: Nicole Vasilevsky Streaming radio online. http://en.wikipedia.org/wiki/Streaming_media embedded controller design An instrument and electronics design technique used to design embedded controllers, small microcontroller typically used in laptops for various purposes. PERSON: Nicole Vasilevsky http://www.coreboot.org/Embedded_controller computer interfacing A technique involving connecting computers and peripherals for usability. Connecting computers to printers and scanners. PERSON: Nicole Vasilevsky http://www.lammertbies.nl/comm/index.html data transfer A data transformation technique involving formatting data for transfer into another software program or hardware. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Transferring data via a USB flash drive. functional autoradiography A autoradiography technique used to describe the first step of the intracellular signal transduction system by visualizing agonist activated receptors by radiolabeling. Analysis of G-protein coupled signaling. PERSON: Nicole Vasilevsky Sovago et al (2001) Brain Research Reviews 38: 149–164 calculation A data transformation technique that involves problem solving for numbers or quantities Calculation of a standard curve. PERSON: Nicole Vasilevsky http://wordnetweb.princeton.edu/perl/webwn?s=calculation concentration calculation A calculation of the concentration of a chemical substance expressed as the amount of the substance present in a mixture. Determining the concentration of a protein based on a protein quantification assay. PERSON: Nicole Vasilevsky http://www.ilpi.com/msds/ref/concentration.html pharmacogenomics assay A nucleic acid assay used to tailor drugs and treatment options to the individual patient by discovering and screening for genetic differences and biomarkers by performing various genetic assays. Lapp (2009) Basic Biotech. 5:1 PERSON: Nicole Vasilevsky Pharmacogenetic assay Pharmacogenetic screening Pharmacogenetic testing Pharmacogenomics screening Pharmacogenomics testing Testing for breast cancer phenotype, such as BrCa positive, Her2/Neu positive, ER positive or triple negative. in vitro pathogenesis assay An organismal assay that conducts systematic, whole-genome screens to identify virulence factors as targets for drug development and exploration of host responses to infections. PERSON: Nicole Vasilevsky Screening of viruses to detect potential targets for therapy. http://ec.asm.org/cgi/content/full/8/8/1218 oestrogen receptor signaling assay A cellular assay designed to study oestrogen receptor signaling by various gene and protein assays in cells or organisms. Detection of estrogen levels in tumor cells. ER signaling assay PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky systems biology analysis A data analysis technique involving study of biology at the system level; the structure and dynamics of cellular and organismal function. Kitano (2002) Science 295:1662 PERSON: Nicole Vasilevsky material component identification An assay that involves identification of components and materials in a mixture. Mass spectrometry. PERSON: Nicole Vasilevsky http://jp.fujitsu.com/group/fql/en/services/rohs/material/ tissue co-culture with ELISA PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Tissue co-culturing combined with ELISA to assay protein expression. in situ hybridization A nucleic acid assay that uses a labeled complementary DNA or RNA strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ), or, if the tissue is small enough (e.g. plant seeds, Drosophila embryos), in the entire tissue (whole mount ISH). ISH PERSON: Nicole Vasilevsky The pattern of gene expression in a developing organism can be analyzed by ISH. http://en.wikipedia.org/wiki/In_situ_hybridization in situ analysis northern blot analysis A nucleic acid assay used in molecular biology research to study gene expression by detection of RNA (or isolated mRNA) in a sample by separating samples by electrophoresis and detection with a hybridization probe complementary to part or the entire target sequence. Gene expression in a sample can be analyzed by Northern blot. Northern blot assay Northern blotting PERSON: Nicole Vasilevsky RNA blot RNA blot analysis RNA blotting http://en.wikipedia.org/wiki/Northern_blot RNA probe A RNA oligonucleotide that is an RNA segment used to probe for a complementary nucleotide sequence either in the mRNA pool or in the DNA of a cell. PERSON: Matthew Brush Placeholder for class to be imported from the Reagent Ontology (ReO). Riboprobe http://www.mondofacto.com/facts/dictionary?riboprobe US resident role A role that inheres in a person who maintains residency in the United states. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky US citizen role A US resident role that inheres in an individual that is a legally recognized as a member of a state, with associated rights and obligations. PERSON: Nicole Vasilevsky http://en.wiktionary.org/wiki/citizen non-US citizen A US resident role that inheres in an individual who is not a legally recognized subject or national of the United States. PERSON: Nicole Vasilevsky https://www.google.com/search?q=residency+status&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-US:official&client=firefox-a#hl=en&client=firefox-a&hs=Bcx&rls=org.mozilla:en-US:official&q=citizen&tbs=dfn:1&tbo=u&sa=X&ei=micXT_DwMIjUiAK15tDUDw&ved=0CCgQkQ4&bav=on.2,or.r_gc.r_pw.,cf.osb&fp=7b67128a22f602af&biw=1609&bih=794 permanent resident role An role that inheres in an individual who is not a citizen but who legally resides in another nation on a permanent or extended basis. PERSON: Nicole Vasilevsky http://connection.ebscohost.com/us/immigration-restrictions/overview-legal-and-illegal-immigration non-permanent resident role A non-US citizen role that inheres in an individual who is residing in a country, but is neither a citizen nor a permanent resident. PERSON: Nicole Vasilevsky http://www.irs.gov/taxtopics/tc851.html student role A college student. A role inhering in a person that is realized when the bearer participates a course of study, as in a school, college, university, etc. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/student undergraduate student role A college student. A student role inhering in a person that is realized when the bearer participates in a course of study at a college, university, etc. in pursuit of an associate or bachelor degree. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/student graduate student role A PhD student at a university. A student role inhering in a person that is realized when the bearer participates a course of study at a university or institution in pursuit of an graduate or professional degree. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/student high school student role A freshman in high school. A student role inhering in a person that is realized when the bearer participates in a course of study at a secondary learning institution. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/student employee role A role inhering in a person that is realized when the bearer participates in an occupation by which a person earns a living or spends their time. An employee at a university. PERSON: Nicole Vasilevsky http://dictionary.reference.com/browse/employment faculty role A professor at a university. An employee role inhering in a person that is realized when the bearer participates in the teaching and/or administrative force of a university, college, or school. PERSON: Nicole Vasilevsky http://dictionary.reference.com/browse/faculty staff role A research technician in a lab. An employee role inhering in a person that is realized when the bearer is employed by an employer. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky post-baccalaureate trainee A student role inhering in a person that is realized when the bearer participates in a post-baccalaureate training program in pursuit of an additional bachelor degree or new or additional training in a particular field. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky yeast two hybrid screening A protein interaction detection assay used to discover 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. PERSON: Nicole Vasilevsky Screening proteins that interact with the activation domain of p53. Yeast two hybrid interaction screening http://en.wikipedia.org/wiki/Two-hybrid_screening restriction enzyme digestion Digestion of DNA at BamHI sites. Enzymatic cleavage of DNA at specific sequences resulting in restriction fragments with restriction enzymes, which are enzymes isolated from bacteria that recognize specific restriction sequences in DNA. Restriction enzymes play a very important role in the construction of recombinant DNA molecules, as is done in gene cloning experiments. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Restriction_enzyme transfection Agent delivery of nucleic acids into cells. Transfection typically involves opening transient pores or holes in the cell membrane, to allow the uptake of material. Transfection can be carried out using calcium phosphate, by electroporation, or by mixing a cationic lipid with the material to produce liposomes, which fuse with the cell membrane and deposit their cargo inside. PERSON: Nicole Vasilevsky Transfection of a cell line with a plasmid expressing a gene of interest. http://en.wikipedia.org/wiki/Transfection anesthesia machine An environment control instrument that is used to support the administration of anaesthesia. It contains a breathing system for delivering a gas mixture, including an anesthetic gas, to a patient for inhalation. An isofluorane machine. PERSON: Nicole Vasilevsky http://www.freepatentsonline.com/5568910.html cage washer An instrument that is used to clean the cages used to house organisms. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky squeeze chute An instrument that is used to restrain large animals. PERSON: Nicole Vasilevsky Used to restrain animals for tail injections. chute stock http://medical-dictionary.thefreedictionary.com/squeeze+chute anaesthetic vaporiser A device that delivers a given concentration of a volatile anaesthetic agent, which is which is generally attached to an anaesthetic machine, commonly used for animal experimentation. PERSON: Nicole Vasilevsky Used for delivering anesthesia to rodents prior to injection. enflurane vaporizer http://en.wikipedia.org/wiki/Anaesthetic_vaporiser isoflurane vaporizer animal ventilator An anesthesia machine with a nose cone. An instrument designed to control air that is breathed through it or to either intermittently or continuously assist or control pulmonary ventilation. PERSON: Nicole Vasilevsky http://www.answers.com/topic/ventilator-203 respirator insect rearing chamber An instrument designed to provide a temperature controlled chamber for insect rearing. PERSON: Nicole Vasilevsky Used to breed insects for experimental purposes. http://www.biocold.com/fp_insect_chambers.php small-animal surgery workstation A workstation used for animal stroke models. An instrument designed to provide a ventilated small animal surgery table that functions to control, capture and exhaust waste anesthesia gases down and away from the face of personnel when connected to negative air source. PERSON: Nicole Vasilevsky http://www.tbjinc.com/Products/Docs/32-26%20DD-ST-M.pdf live trap An instrument that is used to catch live animals. PERSON: Nicole Vasilevsky Trap wild animals for study. http://www.shermantraps.com/ animal cage rack An instrument designed to hold animal cages, while allowing for proper ventillation and access to water. Typically the cage racks have wheels on the bottom for ease of movement. Mouse cages are stored on an animal cage rack. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky tattoo machine An instrument designed to permanently tattoo identifying features such as numbers onto an organism. Laboratory animals can be labeled with a tattoo machine, for identification purposes. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky MASCIS impactor A device designed to deliver graded reproducible spinal cord contusions to an organism. NYU Impactor PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Used to study spinal cord injuries. flow injection system An autosampler used for automated handling of sample and reagent solutions with a strict control of reaction conditions. Flow injection into an HPLC apparatus. PERSON: Nicole Vasilevsky http://www.flowinjection.com/method2.html microbalance A microbalance is an instrument capable of making precise measurements of weight of objects of relatively small mass: of the order of a million parts of a gram. An instrument used to weigh small quantities of a substance. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Microbalance cytospin centrifuge A centrifuge that is used to spin a cell suspension onto a slide for viewing under a microscope. PERSON: Nicole Vasilevsky Used in cytology analysis. http://ricfacility.byu.edu/cytospin.html tabletop centrifuge A centrifuge that sits on top of a tabletop or benchtop and have adaptors for tubes ranging from 0.2-100mls. PERSON: Nicole Vasilevsky Used to spin samples. benchtop centrifuge www.fishersci.com/wps/downloads/segment/.../pdf/Sorvall_TT.pdf mechanical cell lysis device A chromatography pump system used to mechanically lyse cells for rapid intracellular protein extraction. A fast-prep bead beater. PERSON: Nicole Vasilevsky Yun et al (2010) Lab Chip 10:1442-1446. electrophysiology data acquisition system ADInstruments PowerLab/8SP. An instrument used to capture and record analog inputs, digital inputs, temperature, humidity, pulse and logic signals, for electrophysiology. PERSON: Nicole Vasilevsky multichannel acquisition system www.microdaq.com/data-logger/data-acquisition.php electrophoretic transfer cell A transfer apparatus used in a Western blot. An electrophoresis system designed for the electrophoretic transfer of macromolecules such as DNA, RNA or proteins from agarose or polyacrylamide gels to a membrane. PERSON: Nicole Vasilevsky Towbin H, Staehelin T, Gordon J. (1979) Proc Natl Acad Sci U S A. 76(9):4350-4. transfer apparatus cold vapor atomic fluorescence spectrophotometry detector A fluorometer that is used for the analytical technique known as atomic fluorescence spectroscopy (AFS). CVAFS detector PERSON: Nicole Vasilevsky Used to analyze fluorescence from a sample. http://en.wikipedia.org/wiki/Cold_vapour_atomic_fluorescence_spectroscopy serum analyzer A hematology analyzer used to analyze blood serum. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky blood serum analyzer in vivo bioluminescence imaging system An image acquisition instrument that is designed for non-invasive in vivo use, to detect bioluminescence, which is based on the expression of luciferase, the light-emitting enzyme of the firefly Photinus pyralis. After the administration of the substrate luciferin, an ATP- and O2-dependent photochemical reaction occurs, resulting in the release of photons by living cells containing luciferase. This photon emission can be detected by a cooled charge-coupled device (CCD) camera, minutes after the administration of the substrate. Contag et al (1997) Photochem Photobiol 66: 523–531 GFP expressing cells can be visualized by in vivo bioluminescence imaging. PERSON: Nicole Vasilevsky in vivo fluorescence imaging system An image acquisition instrument used to detect fluorescence emission from fluorophores in whole-body living organism. PERSON: Nicole Vasilevsky Rao, Dragulescu-Andrasi, Yao. (2007) Curr Opin Biotechnol. 18(1):17-25. Used to detect GFP in a GFP transgenic mouse. imager A workstation set up with a microscope, digital camera and computer. An instrument that is used for high performance digital imaging and quantitative analysis of labels, such as chemiluminescent, fluorescent, chromogenic, and radioisotopic labels. PERSON: Nicole Vasilevsky http://www.raytest.de/bio_imaging/products/image_station_2000_r/image_station_2000_r.html ultracentrifuge A centrifuge optimized for spinning a rotor at very high speeds, capable of generating acceleration as high as 1,000,000 g (9,800 km/s²). PERSON: Nicole Vasilevsky Used in subcellular fractionation. http://en.wikipedia.org/wiki/Ultracentrifuge ultracentrifuge rotor A device consisting of the rotating part of an ultracentrifuge, which is a high-velocity centrifuge. The ultracentrifuge rotor can hold tubes that are spun around a central axis to separate contained materials of different specific gravities, or to separate colloidal particles or submicroscopic particles. PERSON: Nicole Vasilevsky Part of an ultracentrifuge. http://www.answers.com/topic/ultracentrifuge, http://www.answers.com/topic/centrifuge video dimension analyzer An instrument that is a self-contained video processor designed to provide an analog output proportional to the distance between two features perpendicular to the raster lines, in a televised scene. This hardware edge detector tracks blood vessel diameter, and left and right wall thicknesses using an analog video signal. The principle of the instrument is based on sensing optical density changes of the vessel image at a chosen scan line seen on the TV monitor. PERSON: Nicole Vasilevsky http://vistaelectronicsco.com/viddimanalyzer.shtml, http://www.livingsys.com/video/vda-10.html typhoon fluorescence scanner An instrument which has a multimode scanner with capabilities for storage phosphor, fluorescence, and chemiluminescence detection of gels. The instrument combines laser excitation sources with efficient optics for sensitive fluorescent imaging. Emissions are recorded in an image file for quantitative analysis. PERSON: Nicole Vasilevsky http://imagers.salk.edu/typhoon/typhoon-faq.html temperature controller A heater or air conditioner. An instrument used to maintain the temperature of an enclosed space. PERSON: Nicole Vasilevsky http://www.answers.com/topic/temperature-control skin temperature sensor An instrument which allows one to monitor an organism's skin surface temperature during a procedure. PERSON: Nicole Vasilevsky http://www.smiths-medical.com/catalog/temperature-probes/disposables/skin/skin-temperature-probes.html lab rotator An instrument used for rotation of flasks, test tube racks, beakers, vials, Petri dishes, microwell plates, culture plates, plastic/glass trays, and slides in microbiological, immunological and general clinical applications. Co-IP reactions are allowed to incubate in a lab rotator, at 4C. PERSON: Nicole Vasilevsky http://www.thermoscientific.com/wps/portal/ts/products/detail?navigationId=L10529&categoryId=81886&productId=11954377 roller drum An instrument used for growing mini preps, as well as tissue and bacterial cultures by the roller tube method. PERSON: Nicole Vasilevsky http://www.nbsc.com/rollerdrums.aspx total internal reflection fluorescence instrument An instrument used to observe single molecule fluorescence at surfaces and interfaces. The technique is commonly employed to investigate the interaction of molecules with surfaces. PERSON: Nicole Vasilevsky TIRF instrument http://www.olympusmicro.com/primer/techniques/fluorescence/tirf/tirfhome.html blunt needle end delivery probe An instrument that can be used for surface measurements, inserted into tissue or used for single vessel measurements. PERSON: Nicole Vasilevsky http://www.moor.co.uk/products/monitoring/DRT4/probes crash cart A defibrillator is part of a crash cart. An instrument which has a set of trays/drawers/shelves on wheels used in hospital emergency rooms for transportation and dispensing of emergency medication/equipment at site of medical/surgical emergency for life support protocols. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Crash_cart defibrillator An instrument which delivers a therapeutic dose of electrical energy to the heart. This depolarizes a critical mass of the heart muscle, terminates the arrhythmia, and allows normal sinus rhythm to be reestablished by the body's natural pacemaker, in the sinoatrial node of the heart. Defibrillators can be external, transvenous, or implanted, depending on the type of device used or needed. PERSON: Nicole Vasilevsky Used on a coding patient. http://en.wikipedia.org/wiki/Defibrillation hyfrecator An instrument that is a low-powered medical apparatus used in electrosurgery on conscious patients, usually in an office setting. It works by emitting low-power high-frequency A.C. electrical pulses, via an electrode mounted on a handpiece, directly to the affected area of the body. The amount of output power needed is adjustable, and the device is equipped with different tips, electrodes and forceps, depending on the electrosurgical requirement. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Hyfrecator oocyte clamp An instrument that is designed for two-electrode, whole-cell voltage clamping of Xenopus oocytes. Commonly used as host cells for the study of ion channels. PERSON: Nicole Vasilevsky http://www.warneronline.com/product_info.cfm?id=168&CFID=5491126&CFTOKEN=40558311 molecular assay An assay that generates data about the presence, abundance, structure, function, or activity of biological molecules, or a process that occurs at a molecular level of granularity. PCR. PERSON: Matthew Brush PERSON: Nicole Vasilevsky multiparameter monitor A monitoring device that monitors vital signs, such as temperature, blood pressure, and ECG. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky ECG monitor A monitoring device which non-invasively records the transthoracic interpretation of the electrical activity of the heart over time captured and externally recorded by skin electrodes. PERSON: Nicole Vasilevsky Used to measure heart function. http://en.wikipedia.org/wiki/Electrocardiography cauters An instrument that is a hot iron for searing or cauterizing. Blood vessels are cauterized during surgery to prevent excessive bleeding. PERSON: Nicole Vasilevsky http://www.lexic.us/definition-of/cauter blood pressure transducer A blood pressure cuff. An instrument that provides consistent and accurate readings during invasive blood pressure monitoring. PERSON: Nicole Vasilevsky http://www.utahmed.com/deltran.htm blood pressure monitor A blood pressure cuff. A monitoring device used to measure blood pressure, comprising an inflatable cuff to restrict blood flow, and a mercury or mechanical manometer to measure the pressure. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Blood_pressure_monitor telemetry system An instrument that allows remote measurement and reporting of information. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Telemetry thermomixer A heating instrument that can be programmed to shakes tubes, which usually contain solutions, at a specified speed and for a specified time, in order to mix the contents. A thermomixer can be used to mix and incubate bacterial cultures. PERSON: Nicole Vasilevsky http://vwrlabshop.com/eppendorf-thermomixer-and-thermomixer-r-mixers-brinkmann/p/0020628/ gas mixer An instrument that is used to create custom respiratory gas mixtures. PERSON: Nicole Vasilevsky http://www.cwe-inc.com/images/GSM-3.pdf potentiostat An instrument used to control a three electrode cell and run electroanalytical experiments. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Potentiostat chip programmer An instrument that configures programmable non-volatile circuits. PERSON: Nicole Vasilevsky Programming of circuits, such as EPROMs, EEPROMs, Flashs, PALs, FPGAs or programmable logic circuits. http://en.wikipedia.org/wiki/Programmer_%28hardware%29 hand brake A device for slowing or stopping motion, as of a vehicle, especially by contact friction which is adminstered by hand. An emergency brake in a car. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/brake surface grinder An instrument used to produce a smooth finish on flat surfaces. It is a widely used abrasive machining process in which a spinning wheel covered in rough particles (grinding wheel) cuts chips of metallic or non metallic substance from a workpiece, making a face of it flat or smooth. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Surface_grinding lathe An instrument type which spins the workpiece to perform various operations such as cutting, sanding, knurling, drilling, or deformation with tools that are applied to the workpiece to create an object which has symmetry about an axis of rotation. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Lathe milling machine An instrument which is a machine tool used to machine solid materials. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Milling_machine soxhlet extractor An instrument designed for the extraction of a lipid from a solid material. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Soxhlet_extractor UV-ozone surface cleaner An instrument designed to remove molecular levels of contamination to achieve the cleanest possible probes and surfaces. PERSON: Nicole Vasilevsky http://www.bioforcenano.com/index.php?id=290 spin coater An instrument used to apply uniform thin films to flat substrates by centrifugal force. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Spin_coating spinner mask aligner An instrument used in the production of semiconductor integrated circuits. PERSON: Nicole Vasilevsky http://www.abmfg.com/ accelerated solvent extraction system An instrument which is fully automated and uses common solvents to rapidly extract solid and semisolid samples. Extraction of solvents for histological sample preparation. PERSON: Nicole Vasilevsky http://chromatographyonline.findanalytichem.com/lcgc/App+Notes+Enviro/Accelerated-Solvent-Extraction-Sample-Preparation-/ArticleStandard/Article/detail/479946 gravity convection oven An oven that gently moves air vertically through the oven chamber to heat samples. PERSON: Nicole Vasilevsky http://www.amazon.com/LINDBERG-BLUE-GRAVITY-CONVECTION-MICROPROCESSOR/dp/B003NVENII lipid bilayer workstation An instrument that allows for pico- or nano-scale charge current measurements across an artifical lipid membrane through reconstituted, ion-conducting single channels. Currents are measured via silver electrodes, digitized and amplified. PERSON: Nicole Vasilevsky http://www.instmeth.uni-freiburg.de/methods/iocbc/oe/m-plb-workstation.html beveler machine An instrument consisting of two rules or arms, jointed together at one end, and opening to any angle, for adjusting the surfaces of work to the same or a given inclination. Beveled edges are a common aesthetic nicety added to window panes and mirrors. PERSON: Nicole Vasilevsky bevel square http://www.websters-online-dictionary.org/definitions/bevel?cx=partner-pub-0939450753529744%3Av0qd01-tdlq&cof=FORID%3A9&ie=UTF-8&q=bevel&sa=Search#922 electromyography device A instrument used for evaluating and recording the electrical activity produced by skeletal muscles. PERSON: Nicole Vasilevsky Used to measure muscle function. http://en.wikipedia.org/wiki/Electromyography polygraph A lie detector. An instrument for the simultaneous electrical or mechanical recording of several involuntary physiological activities, including blood pressure, skin resistivity, pulse rate, respiration, etc. PERSON: Melissa Haendel http://en.wikipedia.org/wiki/Polygraph oxygraph system A measurement instrument used to measure oxygen evolution or consumption from liquid-phase samples in cellular respiration and photosynthesis research applications. PERSON: Nicole Vasilevsky http://www.hansatech-instruments.com/oxyg1.htm oxygen electrode micro-iontophoresis device An instrument used to drive positive or negative ions into a tissue, in which two electrodes are placed in contact with tissue, one of the electrodes being a pad of absorbent material soaked with a solution of the material to be administered, and a voltage is applied between the electrodes. PERSON: Nicole Vasilevsky http://encyclopedia2.thefreedictionary.com/iontophoresis stimulus isolator An instrument that provides isolated electrical stimulation to tissues in either constant currents or constant voltages. PERSON: Nicole Vasilevsky http://www.harvardapparatus.com/webapp/wcs/stores/servlet/haicat3_10001_11051_37793_-1_HAI_Categories__37757_37791 stimulator An instrument used for nerve and muscle stimulation procedures. Can be used to study nerve or muscle function. PERSON: Nicole Vasilevsky http://www.grasstechnologies.com/products/stimulators/stims88x.html rapid multi-assay analyzer An instrument used to measure key analytes in clinical research studies, such as glucose, triglycerides, pyruvate, etc. It measures the rate of oxygen consumption, which is directly proportional to the substrate concentration. PERSON: Nicole Vasilevsky http://www.analox.com/downloads/gm7uk.pdf microcapillaries An device consisting of a capillary tube with a very small diameter that is used for various applications including microscopy and HPLC. PERSON: Nicole Vasilevsky http://www.answers.com/topic/capillary CNC Lathe A lathe that is designed to use modern carbide tooling and fully use modern processes. The part may be designed and the toolpaths programmed by the CAD/CAM process, and the resulting file uploaded to the machine, and once set and trialled the machine will continue to turn out parts under the occasional supervision of an operator. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Lathe_%28metal%29 laser doppler flowmeter An image acquisition instrument 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: Nicole Vasilevsky http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy fast protein liquid chromatography instrument A liquid chromatograhy column that is used to separate or purify proteins from complex mixtures. FPLC is a type of liquid chromatography where the solvent velocity is controlled by pumps to control the constant flow rate of solvents. The solvents are accessed through tubing from an outside reservoir. Can be used for protein identification and characterization. FPLC PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Fast_protein_liquid_chromatography microelectrode A measurement device that consists of a very small electrode, often used to study electrical characteristics of living cells and tissues. PERSON: Nicole Vasilevsky http://www.answers.com/topic/microelectrode stadiometer A measurement device that measures the length of curves, dashes, etc., by running a toothed wheel along them. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/stadiometer laser doppler blood flow monitor A measurement device used for non-invasive, continuous measurement of microcirculation. The technique is based on the values of the Doppler Effect of low-power laser light scattered randomly by static structures and moving tissue particulates. PERSON: Nicole Vasilevsky http://www.nlm.nih.gov/cgi/mesh/2010/MB_cgi nitric oxide monitor A measurement instrument that measures nitrogen oxide by employing polarography, which measures concentration of nitrogen oxide in blood and any other portion of a living organism. PERSON: Nicole Vasilevsky http://www.intermedical.co.jp/homepage/products/im/imn-111-e.html respirometry system A flow meter. A measurement instrument that is used to obtain estimates of the rates of metabolism of vertebrates, invertebrates, plants, tissues, cells, or microorganisms via an indirect measure of heat production (calorimetry). PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Respirometry carbon dioxide analyzer A measurement instrument that is used to detect carbon dioxide concentration in a given environment. PERSON: Nicole Vasilevsky Used to measure CO2 levels in an incubator. http://www.thomasnet.com/products/analyzers-carbon-dioxide-1645506-1.html oxygen monitor A measurement device, usually attached to the earlobe or fingertip, that measures the oxygen saturation of arterial blood. PERSON: Nicole Vasilevsky Patients admitted to a hospital are routinely monitored for oxygen levels. blood oxygen monitor http://en.wikipedia.org/wiki/Pulse_oximeter pulse oximeter blood analyzer A hematology analyzer. A measurement device that tests a blood sample for certain predetermined constituents. PERSON: Nicole Vasilevsky http://www.nasa.gov/mission_pages/station/science/experiments/PCBA.html fixed stage microscope A microscope which contains a small platform on a microscope where the specimen is mounted for examination. Commonly used for electrophysiological research, such as patch clamp experiments on nerve cells, examinations of brain sections, and for measuring electrical signals on cells. PERSON: Nicole Vasilevsky http://www.thefreedictionary.com/microscope+stage, http://www.dddmag.com/Product-Axio-Examiner-Fixed-Stage-Microscope-908.aspx surgical microscope A microscope used to visualize fine structures within the area of a surgical procedure. PERSON: Nicole Vasilevsky http://www.zeiss.com/C125716F004E0776/0/3168C434988E2189C1257177006C0635/$File/Innovation_14_18.pdf sample preparation system A microplate dispenser workstation that can be used to distribute quantitative liquid samples with an extraordinary level of precision and reproducibility. PERSON: Richard Pearse PERSON: Scott Hoffmann microwave sample preparation system An instrument used for for sample preparation applications such as digestion, extraction, evaporation or drying of sample materials. Digestion of tissues prior to DNA extraction. PERSON: Nicole Vasilevsky http://www.beverageonline.com/product.mvc/Multiwave-3000-Microwave-Sample-Preparation-P-0001?VNETCOOKIE=NO microwave tissue processor A microwave sample preparation system used for processing tissues for immunohistochemistry and microscopic examination. PERSON: Nicole Vasilevsky Panja, Sriram, Saraswathi, Sivapathasundharam (2007) JOMFP 11: 15-17 CNC milling machine A milling machine tool used to machine solid materials. CNC milling machine has features such as an automatic tool changer (ATC) that includes a tool magazine (carousel), and sometimes an automatic pallet changer (APC). PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Milling_machine machining center mill miller preclinical MRI scanner An MRI scanner which is compact and can sit on a desktop and is used for preclinical magnetic resonance imaging (MRI) within molecular imaging laboratories for routine preclinical and molecular imaging in biomedical and pharmaceutical applications. Can be used for preclinical testing of new drugs, to study effect on the brain. PERSON: Nicole Vasilevsky http://www.dotmed.com/news/story/14254/ PET animal imager A small animal image acquisition device that uses positron emission tomography (PET) for non-invasive, in vivo imaging of small animals for the purposes of research or pre-clinical applications. Can be used to assess cell, tissue, and organ function in vivo in animals after experimental treatment. PERSON: Nicole Vasilevsky http://en.wikipedia.org/wiki/Positron_emission_tomography SPECT animal imager A SPECT scanner that is used for non-invasive, in vivo imaging of small animals for the purposes of research or pre-clinical applications. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky 2D gel electrophoresis apparatus A protein separation apparatus employed for two-dimensional protein separation. An instrument that can be used in proteomics, to run a 2D gel. PERSON: Nicole Vasilevsky PERSON: Nicole Vasilevsky Two-dimensional gel electrophoresis apparatus end over end rotator A lab rotator that provides provide 360° vertical rotation, used to mix samples. Can be used to mix samples during a co-IP reaction. PERSON: Nicole Vasilevsky http://www.selectscience.net/products/end-over-end-rotator/?prodID=11939 electromyography stimulator An instrument used to stimulate the electrical activity of muscles. PERSON: Nicole Vasilevsky