Advisors to be Named Aaron Lucas Gem Yang Raimond Winslow This purpose of this ontology is to describe electrophysiological experiments and data. This ontology was created as part of the CardioVascular Research Grid (CVRG) project which is funded through an R24 Resource from the National Heart Lung and Blood Institute (NHLBI). OWL-DL, RDF/XML-ABBREV Free, Open source Electrophysiology Ontology Second Revision 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. An entity responsible for making contributions to the content of the resource. Contributor 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. Coverage 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. An entity primarily responsible for making the content of the resource. Creator 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. A date associated with an event in the life cycle of the resource. Date 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. An account of the content of the resource. Description 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). The physical or digital manifestation of the resource. Format 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). An unambiguous reference to the resource within a given context. Resource Identifier 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. A language of the intellectual content of the resource. Language 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. An entity responsible for making the resource available Publisher 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. Relation 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. Rights Management 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. A reference to a resource from which the present resource is derived. Source 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. The topic of the content of the resource. Subject and Keywords Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Title 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. The nature or genre of the content of the resource. Resource Type DIRECTED-BINARY-RELATION PAL-CONSTRAINT FMA:FMA_20019 FMA:FMA_67498 FMA:FMA_68646 FMA:FMA_9637 ATPDependentCalciumPump This subclass of P-TypeIonPump describes a specific type of ion pump that utilizes ATP to transport Ca2+ ions across a membrane. ATPDependentSodiumPump This subclass of P-TypeIonPump describes a specific type of ion pump that utilizes ATP to transport Na+ ions across the plasma membrane also known as a sodium potassium pump because this type of pump maintains cell potential by contolling the concentrations of both Na+ and K+ ions with the cell. AlphaSubunit This subclass of Subunit describes a naming convention used to allow scientists to explain the different types/kinds of protein subunits that come together to create complexes. The greek letter alpha in this case denotes a specific subunit with a certain complex Amplifier http://dictionary.reference.com/ This subclass of Device describes an electronic component or circuit for amplifying power, current, or voltage Anesthesia http://dictionary.reference.com This subclass of SingleProcedure describes a general or local insensibility, as to pain and other sensation, induced by certain interventions or drugs to permit the performance of surgery or other painful procedures. Animal This subclass of Biomaterial represents a multicelular organism that is a member of the kingdom Animalia. Article The research paper from which this EPStudy is created. BackgroundRegulator This subclass of Regulator is also known as a leaky channel. BeforeAfterObservation This subclass of Observation defines where an observable event was measured at two time points in comparative studies. BetaSubunit This subclass of Subunit describes a naming convention used to allow scientists to explain the different types/kinds of protein subunits that come together to create complexes. The greek letter beta in this case denotes a specific subunit with a certain complex. BinaryQuantity This subclass of Quantity consists of two SingularQuantitys and a relationship between them. Biomaterial This class represents the important substances such as cells, tissues organs, proteins, etc. Biomaterials can be linked to one another though the subclass PairedBiomaterial which allows exactly 2 different biomaterials to be connected. Biomolecule This subclass of Biomaterial encompasses chemical molecules that naturally occurs in living organisms. Biomolecules consist primarily of carbon and hydrogen, along with nitrogen, oxygen, phosphorus and sulfur. BufferedSolution Ca This subclass of PermeantIon describes calcium ions. CaCh This subclass of Gene describes genes that encode for PM calcium pump subunits. CalciumAlpha1Subunit Birnbaumer L, Qin N, Olcese R, Tareilus E, Platano D, Costantin J, Stefani E. Structures and functions of calcium channel beta subunits. J Bioenerg Biomembr. 1998 Aug; 30(4):357-75. Review. This subclass of AlphaSubunit describes the subunit that is responsible for forming the ion conducting pore and has voltage sensing and drug//toxin binding properties in the calcium channel complex, and is considered the primary subunit of the complex. This subunit is structurally comprised of four homologous domains each containing six transmembrane helices. The fourth transmembrane helix of each domain forms a voltage sensor. CalciumAlpha2DeltaSubunit Jones, S.W. Overview of voltage-dependent calcium channels. J Bioenerg Biomembr. 1998 Aug; 30(4):299-312. Review. This subclass of Subunit describes the most often found complex between the alpha 2 and delta subunits that form calcium channel complex. This complex is a proteolytically processed disulfide linked dimer that originates from a single precursor mRNA. CalciumAlpha2Subunit [1] http://www.chemsoc.org/exemplarchem/entries/2002/tim_smith/channels/calcium/ [2] Tseng TT, McMahon AM, Zahm RJ, Pacold ME, Jakobsson E. Calcium channel auxiliary subunits. J Mol Microbiol Biotechnol. 2006; 11(6):326-44. Review. This subclass of AlphaSubunit describes the subunit that is a highly glycosylated extracellular protein that is attached to the membrane-spanning delta-subunit by means of disulfide bonds[1]. The alpha 2 subunit also provides structural support and increases functionmal diversity of the calcium channel complex[2]. CalciumBetaSubunit http://www.chemsoc.org/exemplarchem/entries/2002/tim_smith/channels/calcium/ This subclass of BetaSubunit describes the calcium channel subunit that is situated intracellularly and is involved in the membrane trafficking of alpha 1subunits CalciumChannel http://en.wikipedia.org This subclass of IonChannel describes the group of channels that have a permeability to Ca2+ ions. These channels consist of a complex of different subunits whereby the alpha-1 subunit forms the ion conducing pore while other associated subunits can modulate gating. CalciumDeltaSubunit http://www.chemsoc.org/exemplarchem/entries/2002/tim_smith/channels/calcium/ This subclass of DeltaSubunit describes the membrane-spanning calcium channel subunit that modulates the voltage-dependent activation and steady-state inactivation of the channel andt is attached to the alpha 2 subunit by means of disulfide bonds. **second draft addition CalciumGammaSubunit http://www.chemsoc.org/exemplarchem/entries/2002/tim_smith/channels/calcium/ This subclass of GammaSubunit is a glycoprotein subunit of the calcium channel complex having four transmembrane segments. **second draft addition Cannulation This subclass of SingleProcedure describes a process whereby a metal tube is inserted into the body to draw off fluid or to introduce medication. CapacitanceCompensation This subclass of SingleProcedure describes the act of applying a compensation voltage that causes a current which is equal and opposite to the current through any stray capacitance between terminal leads Cell [1] http://en.wikipedia.org [2] http://sig.biostr.washington.edu/projects/fm/AboutFM.html This subclass of Biomaterial describes the structural and functional unit of all known living organisms. It is the simplest unit of an organism that is classified as living, and is sometimes called the building block of life. [1] This class references the Foundation Model of Anatomy class label Cell. [2] CellAttachedPatchClamp CellAttachedPatchElectrode This subclass of PatchClampElectrode describes an electrode that Chamber This subclass of Device describes an appartus that warms, oxygenates, and perfuses tissue. ChebiID http://www.ebi.ac.uk/chebi/ This subclass of ID describes external database references to the Chemical Entities of Biological Interest (ChEBI) which is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. Cloned This subclass of GeneType references a gene that has be duplicated from another organism, an exact copy of its DNA makeup. CompositeSolution Compound http:en.wikipedia.org This class describes a substance that arises from the combination of at least two elements that are chemically bonded to one another. ConfocalMicroscope http://en.wikipedia.org This subclass of LightMicroscope is a microscope used to increase micrograph contrast and/or to reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light or flare in specimens that are thicker than the focal plane. CurrentClamp DbSnpID http://www.ncbi.nlm.nih.gov/projects/SNP/ This subclass of ID describes external database references to the Single Nucleotide Polymorphism database (dbSNP) which is a public-domain archive for a broad collection of simple genetic polymorphisms. DeltaSubunit This subclass of Subunit describes a naming convention used to allow scientists to explain the different types/kinds of protein subunits that come together to create complexes. The greek letter delta in this case denotes a specific subunit with a certain complex. Depolarization http://en.wikipedia.org This subclass of SingleProcedure describes an act whereby an observer decreases the absolute value of a cell's membrane potential. Thus, changes in membrane voltage in which the membrane potential becomes less positive or less negative are both depolarizations. Device This class describes a biological instrument that is used to perform one or more relatively simple tasks. Disaggregation This subclass of SingleProcedure describes a process whereby a component is broken into smaller parts or to subdivide it. Dissection This subclass of SingleProcedure describes the act of separating or dividing for the purpose of critical examination. EPStudy This class is the main class for an Electrophysiological Study. A EPStudy has four targets, a Creator, a Biomaterial, a Procedure, and an Observation. Looking at this ontology at a hierarchical view, the class EPStudy would be the top node. Electrode http://dictionary.reference.com This subclass of Device describes a solid electric conductor through which an electric current enters or leaves an electrolytic cell or other medium. ElectronMicroscope http://dictionary.reference.com/ This subclass of Microscope is a microscope of extremely high power that uses beams of electrons focused by magnetic lenses instead of rays of light, the magnified image being formed on a fluorescent screen or recorded on a photographic plate: its magnification is substantially greater than that of any optical microscope. Emplacing This subclass of SingleProcedure describes a EnsemblGeneID http://www.ensembl.org/index.html This subclass of ID describes external database references to the joint project between EMBL - European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. EnsemblProteinID http://www.ensembl.org/index.html This subclass of ID describes external database references to the joint project between EMBL - European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) to develop a software system which produces and maintains automatic annotation on selected eukaryotic proteomes. EntrezGeneID http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene This subclass of ID describes external database references to the searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer Enzyme http://en.wikipedia.org This subclass of Protein describes the best known role of a protein which is to catalyze chemical reations. Excision This subclass of SingleProcedure describes the surgical removal of a substance such as a tissue or organ. ExtracellularRecording This subclass of Recording describes a process one will preserve evidence from measurements made about recordings from outside the cell membrane. Filtration The American Heritage Dictionary of the English Language, Fourth Edition This subclass of SingleProcedure describes the act or process of filtering. FluorescenceImaging FluorescenceMicroscope http://en.wikipedia.org This subclass of LightMicroscope is a 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. Fluorometry http://dictionary.reference.com This subclass of SingleProcedure describes the act of measuring fluorescence, often as a means of determining the nature of the substance emitting the fluorescence. GOID http://www.geneontology.org/ This subclass of ID describes external database references to the Gene Ontology Consortium which is a controlled vocabulary to describe gene and gene product attributes in any organism GammaSubunit This subclass of Subunit describes a naming convention used to allow scientists to explain the different types/kinds of protein subunits that come together to create complexes. The greek letter gamma in this case denotes a specific subunit with a certain complex. Gene http://dictionary.reference.com This subclass of Biomolecule describes a linear sequence of nucleotide along a segment of DNA that is the basic physical unit of heredity. GeneCardID http://www.genecards.org/index.shtml This subclass of ID describes external database references to an integrated database of human genes that includes automatically-mined genomic, proteomic and transcriptomic information, as well as orthologies, disease relationships, SNPs, gene expression, gene function, and service links for ordering assays and antibodies. GeneType This subclass of Qualifer decribes the linage/origination of a particular gene. Heterozygous http://en.wikipedia.com This subclass of Zygosity describes a condition when an organism has different alleles occupying a specific gene's position in each of the homologous chromosomes. In other words, it describes an individual that has 2 different alleles for a trait. Example Pp - where P and p refer to different alleles of the same gene. HgncID http://www.genenames.org/ This subclass of ID describes external database references to the HUGO Gene Nomenclature Committee which for each known human gene, approve a gene name and symbol (short-form abbreviation). Homeostasis http://dictionary.reference.com This subclass of Observation describes the ability or tendency of an organism or cell to maintain internal equilibrium by adjusting its physiological processes HomoloGeneID www.ncbi.nlm.nih.gov/sites/entrez?db=homologene This subclass of ID describes external database references to an anutomated system for detecting homologs among eukaryotic gene sets Homozygous http:\\en.wikipedia.com This subclass of Zygosity describes a condition where an organism at a specific locus, carries two identical copies of the gene affecting a given trait on the two corresponding homologous chromosomes. Example PP or pp - where P and p refer to different alleles of the same gene. HprdID http://www.hprd.org/ This subclass of ID describes external database references to the Human Protein Reference Database which represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome Hyperpolarization http://dictionary.reference.com This subclass of SingleProcedure describes the act of increasing the difference in electric potential across (a cell membrane) ID This class holds subclass of identifiers to external database references. I_CaL This subclass of IonCurrent is the variable used for measuring L-type calcium current. I_CaT This subclass of IonCurrent is the variable used for measuring T-type calcium current. I_K This subclass of IonCurrent is the variable used for measuring delayed rectifier potassium current. Total iK is composed of the rapidly activating iKr and the slowly activating iKs. I_K1 This subclass of IonCurrent is the variable used for measuring inwardly rectifing potassium current. I_Kp This subclass of I_K is the variable used for measuring plateau potassium current I_Kr This subclass of I_K is the variable used for measuring rapidly activating potassium current. I_Ks This subclass of I_K is the variable used for measuring slowly activating potassium current. I_Kur This subclass of I_K is the variable used for measuring ultrarapid outward potassium current. I_Na This subclass of IonCurrent is the variable used for measuring rapid sodium current I_NaCa This subclass of IonCurrent is the variable used for measuring the sodium-calcium exchanger current. I_NaK This subclass of IonCurrent is the variable used for measuring the sodium-potassium pump current I_pCa This subclass of IonCurrent is the variable used for measuring calcium pump current. I_to1 This subclass of IonCurrent is the variable used for measuring transient outward potassium current. It has at least two distinct transient outward K+ currents, I to, fast and I to, slow. I_to2 This subclass of IonCurrent is the variable used for measuring transient outward chloride current. Immersion This subclass of SingleProcedure describes the act of placing a substance below a liquid medium. Implantation http://dictionary.reference.com This subclass of SingleProcedure describes the act of inserting or grafting a tissue, organ, or inert substance into the body. InsideOutPatchClamp InsideOutPatchElectrode This subclass of PatchClampElectrode describes an electrode that InterProID http://www.ebi.ac.uk/interpro/ This subclass of ID describes external database references to protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. IntracellularRecording This subclass of Recording describes a process one will preserve evidence from measurements made about recordings from within the cell membrane InvertedMicroscope http://en.wikipedia.org This subclass of LightMicroscope is a microscope with its light source and condenser on the top above the stage pointing down, and the objectives and turret are below the stage pointing up. InwardRectifierPotassiumChannel http://en.wikipedia.org This subclass of PotassiumChannel describes potassium selective channels that recitfy current in the inward direction, they pass more current inward than outward IonChannel http://en.wikipedia.org This subclass of Biomolecule describes pore-forming proteins that help to establish and control the small voltage gradient across the plasma membrane of all living cells by allowing the flow of ions down their electrochemical gradient. They are found in membrands that surrond all biological cells. IonCurrent This subclass of Data defines the electric current resulting from motion of ions. IonExchanger This subclass of IonExchanger uses the gradient of one ion to transport another ion against its gradient, also called a cotransporter. IonTransporter This subclass of Biomolecule describes transmembrane proteins that move ions across the plasma membrane against their concntration gradient, also called "ion pumps" Isolation http://dictionary.reference.com This subclass of SingleProcedure describes the act of to setting or placing something apart; detach or separate so as to be alone. K This subclass of PermeantIon describes potassium ions. KCh This subclass of Gene describes genes that encode for potassium channel subunits. KEGGID http://www.genome.jp/kegg/ This subclass of ID describes external database references to the Kyoto Encyclopedia of Genes and Genomes which is a database of biological systems, consisting of genetic building blocks of genes and proteins (KEGG GENES), chemical building blocks of both endogenous and exogenous substances (KEGG LIGAND), molecular wiring diagrams of interaction and reaction networks (KEGG PATHWAY), and hierarchies and relationships of various biological objects (KEGG BRITE). KEGG provides a reference knowledge base for linking genomes to biological systems and also to environments by the processes of PATHWAY mapping and BRITE mapping. L-TypeCalciumChannel http://en.wikipedia.org This subclass of CalciumChannel describes calcium channels that are high-voltage activiated and have slow inactivation kinetics, whereby the L stands for "long-lasting". Lamp http://dictionary.reference.com/ This subclass of Device describes any of various devices furnishing artificial light. LigandGatedChannel http://en.wikipedia.org This subclass of IonChannel describes a group of intrinsic transmembrane ion channels that are opened or closed in response to binding of a chemical messenger, also referred to as LGICs, or ionotropic receptors. LigandRegulator This subclass of Regulator is a chemical compound that regulates ion channel activity. LightMicroscope This subclass of Microscope is a microscope that uses a rays of light instead of electrons to illuminate the subject of interest. MechanoRegulator This subclass of Regulator cellular forces that regulate the ion channel activity, such as membrane stretching. MgiID http://www.informatics.jax.org/ This subclass of ID describes external database references to the Mouse Genome Informatics (MGI) Database that provides integrated access to data on the genetics, genomics and biology of the laboratory mouse. Microscope http://dictionary.reference.com/ This subclass of Device is an optical instrument having a magnifying lens or a combination of lenses for inspecting objects too small to be seen or too small to be seen distinctly and in detail by the unaided eye. MultiPhotonMicroscope This subclass of FluorescenceMicroscope is a microscope that uses pulsed long wavelength laser light to excite fluorophores within a specimen. The fluorophore absorbs the energy from two long-wavelength photons that must arrive simultaneously in order to excite an electron into a higher energy state, from which it can decay, emitting a fluorescence signal. It differs from traditional fluorescence microscopy in which the excitation wavelength is shorter than the emission wavelength, as the summed energies of two long-wavelength exciting photons will produce an emission wavelength shorter than the excitation wavelength. MultipleCellExtracellularRecording This subclass of ExtracellularRecording describes a process one will preserve evidence from measurements made about recordings from outside the cell membrane of multiple cells. Mutant http://en.wikipedia.org This subclass of Gene describes a class of genes that have lost, gained, or exchanged some of their DNA that results in the creation of a new trait or character. These traits differ from the norm.) Na This subclass of PermeantIon describes sodium ions. NaCh This subclass of Gene describes genes that encode for sodium channel subunits. NaKAlphaSubunit http://www.vivo.colostate.edu/hbooks/molecules/sodium_pump.html This subclass of AlphaSubunit desribes the sodium/potassium pump subunit that binds ATP, sodium and potassium ions, and contains the phosphorylation site for the pump. NaKBetaSubunit http://www.vivo.colostate.edu/hbooks/molecules/sodium_pump.html This subclass of BetaSubunit is absolutely necessary for activity of the sodium potassium pump complex. It appears to be critical in facilitating the plasma membrane localization and activation of the alpha subunit. The beta subunit is can be glycosylated. NaKGammaSubunit Beguin P, Wang X, Firsov D, Puoti A, Claeys D, Horisberger JD, Geering K. The gamma subunit is a specific component of the Na,K-ATPase and modulates its transport function. EMBO J. 1997 Jul 16; 16(14):4250-60. This subclass of GammaSubunit is has been described since 1978 and to this date can be found in complexes with both the alpha and beta subunits of the sodium potassium pump complex, but yet to date not much is known about it. Observation "observation." The Oxford Dictionary of Sports Science . Oxford University Press, 1998, 2006, 2007. Answers.com 15 Oct. 2007. http://www.answers.com/topic/observation This class describes the deliberate act of an observer who studies events using his or her sensory processes as well as data obtained from scientific recordings/measurements. An observation is usually the first step taken in a scientific investigation. OmimID This subclass of ID describes external database references to the Online Mendelian Inheritance in Man which is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information and references. It also contains copious links to MEDLINE and sequence records in the Entrez system, and links to additional related resources at NCBI and elsewhere. Organ [1] http://en.wikipedia.org [2] http://sig.biostr.washington.edu/projects/fm/AboutFM.html This subclass of Biomaterial describes a group of tissues which perform some function. [1] This class references the Foundation Model of Anatomy class label Organ. [2] OtherSubunit This subclass of Subunit is a class created for an unclassified type of subunit. OutsideOutPatchElectrode This subclass of PatchClampElectrode describes an electrode that P-TypeIonPump This subclass of IonTransporter describes a group of ion pumps that all utilize ATP as an energy source and all contain phosphorylated intermediates of an aspartyl residue (this is why they are called P-type pumps) The phosphate is donated by an ATP molecule and forces the pump into a high-energy intermediate state. The energy stored in the high energy form of the protein is then used to translocate ions. PMCA This subclass of Gene describes genes that encode for PM calcium pump subunits. PMCalciumPump This subclass of ATPDependentCalciumPump describes a class of ion pump that uses ATP to pump Ca2+ ions across the plasma membrane (PM). PaceMaker http://en.wikipedia.org This subclass of Device is an implanted medical device which uses electrical impulses, delivered by electrodes contacting the heart muscles, to regulate the beating of the heart. Pacing This subclass of SingleProcedure describes the act of applying electric shocks to the heart, so that a regular rhythm can be restored PairedObservation This subclass of Observation describes where one type of observation is described from two sources. e.g. one would like to express that a channel current differs in control versus diseased hearts or, from wildtype vs recombinant channels, or normal vs mutant species. ParallelProcedure This subclass of Procedure describes the procedures that are carried out on a particular biomaterial in unison. A particular biomaterial may have two seperate series of procedures carried out upon it at the same time. PatchClamp PatchClampElectrode http://en.wikipedia.org This subclass of Electrode describes an electrode that traditionally uses a glass pipette, with an open tip diameter of about one micrometre, and is made such that the tip forms a smooth surfaced circle, rather than a sharp point. PdbID http://www.pdb.org/pdb/home/home.do This subclass of ID describes external database references to the RCSB Protein Data Bank which is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids. PerforatedPatchElectrode This subclass of PatchClampElectrode describes an electrode that Perfusion This subclass of SingleProcedure describes the passage of fluid through a biomaterial, such as an organ, tissue, or cell. PermeantIon This subclass of Qualifier desscribes they types of ions that can be carried across a membrane by ion channels/pumps. Person http://dictionary.reference.com This class reperesents a human being as distinguished from an animal or a thing PfamID http://pfam.sanger.ac.uk/ This subclass of ID describes external database references to the Sanger Institutes database which is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) Pharmacologic This subclass of Qualifier describes a specific drug that has a desired outcome in the treatment of an organism. PhotoMultiplier http://en.wikipedia.org This subclass of Device is a device that is an extremely sensitive detector of light in the ultraviolet, visible and near infrared. PotassiumAlphaSubunit http://en.wikipedia.org This subclass of AlphaSubunit is the subunit that is part of the potassium channel comple and is know to have six transmembrane segments, homologous to a single domain of the sodium channels. Correspondingly, they assemble as tetramers to produce a functioning channel and have a distinctive pore-loop structure that lines the top of the pore and is responsible for potassium selectivity. PotassiumBetaSubunit http://en.wikipedia.org This subclass of BetaSubunit is a potassium channel subunit that determines the potential-sensitivity and inactivation properties of the potassium channel complex. PotassiumChannel http://en.wikipedia.org This subclass of IonChannel describes the group of channels that have a permeability to K+ ions. The pore-forming subunits of potassium channels have a homo- or heterotetrameric arrangement. Four subunits are arranged around a central pore. All potassium channel subunits have a distinctive pore-loop structure that lines the top of the pore and is responsible for potassium selectivity. PrintsID http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/ This subclass of ID describes external database references a database that houses a collection of protein fingerprints, which may be used to assign family and functional attributes to uncharacterised sequences, such as those currently emanating from the various genome-sequencing projects Procedure This class describes the sequence of actions or instructions to be followed in solving a problem or accomplishing a task. http://dictionary.reference.com PrositeID http://www.expasy.ch/prosite/ This subclass of ID describes external database references which consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them Protein http://en.wikipedia.org This subclass of Biomolecule describes large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. PubMedID http://www.ncbi.nlm.nih.gov/sites/entrez?db=PubMed This subclass of ID describes external database references to the U.S. National Library of Medicine that includes over 17 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources. Qualifier This class describes the types other classes, differentiates from the notion of multiple inheritance. Quantity This class is abstract. The word quantity dose not imply its traditional meaning i.e. one value and one unit. The subclasses have precise definition of number of values. RawDataFile This subclass of Observation holds the location of the raw data file used during the particular study. Recombinant This subclass of GeneType decribes genes of a type resulting from the artificial insertion of DNA into existing DNA coding stands, creating a "man-made" form of a gene. RecombinantChannel This subclass of IonChannel describes ion channels resulting from the artificial insertion of DNA into existing DNA coding stands, creating a "man-made" form of a gene that encodes a ion channel. RecombinantCurrent This subclass of IonCurrent describes current measurements acquired from ion channels/ transporters, that have been created by the artificial insertion of DNA into existing DNA coding stands, creating a "man-made" form of a gene that encodes the particular ion channel or transporter RecombinantGene http://en.wikipedia.org This subclass of Gene describes genes resulting from the artificial insertion of DNA into existing DNA coding stands, creating a "man-made" form of a gene, these genes are not the result of a natural process they are engineered. RecombinantProtein This subclass of Protein describes proteins resulting from the artificial insertion of DNA into existing DNA coding stands, creating a "man-made" form of a gene that that is later translated into a protein. RecombinantSpliceVariant This subclass of SpliceVariant describes subunits resulting from the artificial insertion of DNA into existing DNA coding stands, creating a "man-made" form of a gene that encodes a subunit. RecombinantSubunit This subclass of Subunit describes subunits resulting from the artificial insertion of DNA into existing DNA coding stands, creating a "man-made" form of a gene that encodes a subunit. RecombinantTransporter This subclass of IonTransporter describes ion transporters resulting from the artificial insertion of DNA into existing DNA coding stands, creating a "man-made" form of a gene that encodes a ion transporter. Recording http://dictionary.reference.com This subclass of SingleProcedure describes a process where one will set down in writing or the like, as for the purpose of preserving evidence, particularly in electrophysiological experiments. RectilinearInjection This subclass of SingleProcedure describes a RefSeqID http://www.ncbi.nlm.nih.gov/RefSeq/ This subclass of ID describes external database references to the Reference Sequence collection that aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms. ReflectionElectronMicroscope http://en.wikipedia.org This subclass of ElectronMicroscope is a microscope that involves electron beams incident on a surface, but instead of using the transmission (TEM) or secondary electrons (SEM), the reflected beam is detected. Regulator The American Heritage Dictionary of the English Language, Fourth Edition. This subclass of Qualifier describes a substance that affects the amount of product or the progress of a biochemical reaction or process, spefically ion channel activity. Resting This subclass of SingleProcedure describes the act ofallowing a substance to remain in place, without activity or movement. RgdID http://rgd.mcw.edu/ This subclass of ID describes external database references to the Rat Genome Database (RGD) that curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease SRCalciumPump This subclass of ATPDependentCalciumPump describes a class of ion pump that uses ATP to pump Ca2+ ions across the sarcoplasmic reticulum (SR) ScanningElectronMicroscope http://en.wikipedia.org This subclass of ElectronMicroscope is a microscope that is capable of producing high-resolution images of a sample surface. The SEM produces images by detecting low energy secondary electrons which are emitted from the surface of the specimen due to excitation by the primary electron beam ScanningTransmissionElectronMicroscope http://en.wikipedia.org This subclass of ElectronMicroscope, STEM combines the high resolution of the TEM with the beam rastering functions of the SEM, allowing a range of analytical techniques to be used that are not possible with conventional TEM. ScopID This subclass of ID describes external database references to the Structural Classification of Proteins database that database aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known, including all entries in the Protein Data Bank (PDB) SerialProcedure This subclass of Procedure describes the procedures that are carried out on a particular biomaterial in a time/order dependent series. This type of procedure takes into account the order in which procedures are carried out upon a biomaterial, ie the workflow. SharpElectrode This subclass of Electrode describes an electrode that SharpElectrodeVoltageClamp SingleCellExtracellularRecording This subclass of ExtracellularRecording describes a process one will preserve evidence from measurements made about recordings from outside the cell membrane of a single cell. SingleCellRecording This subclass of Recording describes a process where one will set down in writing or the like, as for the purpose of preserving evidence, particularly in electrophysiological experiments the activity of at most one cell. SingleElectrodeVoltageClamp SingleProcedure This subclass of Procedure describes various single procedures that can be carried out upon a biomaterial. This class only takes into account one procedure at a time. Thes procedures may be linked in either a time/order dependant (serial) or parallel framework. SingularQuantity This subclass of Quantity describes a class that consists of one number and one unit. Soaking http://dictionary.reference.com This subclass of SingleProcedure describes the act of allowing a substance to lie in and become saturated or permeated with a liquid. SodiumAlphaSubunit http://en.wikipedia.org This subclass of AlphaSubunit is the subunit of a the sodium channel that is responsible for selectivity and voltage gating and has four repeat domains, labeled I through IV, each containing six membrane-spanning regions, labeled S1 through S6. The highly conserved S4 region acts as the channel's voltage sensor. SodiumBeta1Subunit http://en.wikipedia.org This subclass of BetaSubunit describes a sodium channel subunit that when assembled with alpha subunits the resulting complex can display altered voltage dependence and cellular localization. SodiumBeta2Subunit http://en.wikipedia.org This subclass of BetaSubunit describes a sodium channel subunit that when assembled with alpha subunits the resulting complex can display altered voltage dependence and cellular localization SodiumBeta3Subunit http://en.wikipedia.org This subclass of BetaSubunit describes a sodium channel subunit that when assembled with alpha subunits the resulting complex can display altered voltage dependence and cellular localization **second draft addition SodiumBeta4Subunit http://en.wikipedia.org This subclass of BetaSubunit describes a sodium channel subunit that when assembled with alpha subunits the resulting complex can display altered voltage dependence and cellular localization **second draft addition SodiumCalciumExchanger http://en.wikipedia.org This subclass of IonExchanger is an antiporter membrane protein which removes calcium from cells and does not use ATP in the process. SodiumChannel http://en.wikipedia.org This subclass of IonChannel describes the group of channels that have a permeability to Na+ ions. Sodium channels are a complex of two types of protein subunits, alpha and beta, whereby the former forms the core of the channel. The alpha subunit contains 4 homologous domains and all of the subunits belonging to a soduim channel can be modified by glycosylation. SodiumGlucoseCotransporter http://en.wikipedia.org This subclass of IonExchanger uses energy from a downhill sodium gradient to transport glucose across the apical membrane against an uphill glucose gradient. SodiumHydrogenExchanger This subclass of IonExchanger uses energy from a downhill sodium gradient to eject protons from cells therebyregulating pH , cell volume, and cellular response to many different hormones and mitogens. Solute This class consists of a chemical substance and a SingularMeasurement. Solution Species SpliceVariant http://en.wikipedia.org This subclass of Biomolecule decribes mRNA that is alternatively transcripted from a gene. The exons from a gene transcripted are arranged alternatively. StandardDeviation This subclass of SingularQuantity describes a class with a statistical measure of the dispersion or variation in a distribution StrongInwardRectifierPotassiumChannel This subclass of InwardRectifierPotassiumChannel describes a potassium channel that maintains a stabilizing effect over a voltage range of 50 mV positive to EK. Subunit http://en.wikipedia.org This subclass of Protein is a single protein molecule that assembles (or "coassembles") with other protein molecules to form a multimeric or oligomeric protein. Superfusing http://www.m-w.com This subclass of SingleProcedure describes a procedure to maintain the metabolic or physiological activity of (as an isolated organ) by submitting to a continuous flow of a sustaining medium over the outside SwissProtID http://expasy.org/sprot/ This subclass of ID describes external database references to a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases T-TypeCalciumChannel http://en.wikipedia.org This subclass of CalciumChannel describes calcium channels that are transient or low voltage activated and have rapid inactivation kinetics, whereby the T stands for "transient" Technique Temperature This subclass of SinglarQuantityis a class that is expressed in a unit of celsius or fahrenheit. Thoracotomy http://dictionary.reference.com This subclass of SingleProcedure describes the procedure of a sugical incision into the chest wall. Tissue This subclass of Biomaterial describes a group of biological cells that perform a similar function. [1] [1] http://en.wikipedia.org [2] http://sig.biostr.washington.edu/projects/fm/AboutFM.html This class references the Foundation Model of Anatomy class label Tissue. [2] Transfection http://www.m-w.com This subclass of SingleProcedure describes the procedure of incorporating exogenous DNA into a cell. TransmissionElectronMicroscope http://en.wikipedia.org This subclass of ElectronMicroscope is a microscope that uses a beam of electrons is transmitted through a specimen, then an image is formed, magnified and directed to appear either on a fluorescent screen or layer of photographic film, or to be detected by a sensor such as a CCD camera. Also known as TEM, the transmission electrons are what are being detected. TwoElectrodeVoltageClamp TwoPhotonMicroscope http://en.wikipedia.org This subclass of MultiPhotonMicroscope is a microscope that uses two photons of low energy that 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. The probability of the near-simultaneous absorption of two photons is extremely low. Therefore a high flux of excitation photons is typically required, usually a femtosecond laser, allowing imaging of living tissue up to a depth of one millimeter. This microscope allows for a viable alternative to confocal microscopes due to deeper tissue penetration and reduced phototoxicity. UniProtID http://www.pir.uniprot.org/ This subclass of ID describes external database references to the Universal Protein Resource which is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UnigeneID http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene This subclass of ID describes external database references to the NCBi's Unigene database that is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. UprightMicroscope This subclass of LightMicroscope is a microscope where the illumination system is below the stage and the lens system is above the stage. Vendor VoltageClamp VoltageGatedChannel http://en.wikipedia.org This subclass of IonChannel describes a class of transmembrane ion channels that are activated by changes in electrical potential difference near the channel. VoltageRegulator This subclass of Regulator, the voltage regulates the ion channel activity. WaveformInjection This subclass of SingleProcedure describes a Wavelength This subclass of SingularQuantity describes a class that states measurements of distance between crests of a wave. WeakInwardRectifierPotassiumChannel This subclass of InwardRectifierPotassiumChannel describes a potassium channel that maintain their stabilizing effect virtually over the whole physiological voltage range. WholeCellPatch WholeCellPatchElectrode This subclass of PatchClampElectrode describes an electrode that WholeCellRecording This subclass of Recording describes a process where one will set down in writing or the like, as for the purpose of preserving evidence, particularly in electrophysiological experiments; measurements before the cell has been dialyzed. Whole-cell recordings involve recording currents through multiple channels at once. WildType This subclass of GeneType describes genes of a type that are not man-made, they are not engineered, they are in fact genes that are typically found/occur in nature. WildTypeChannel This subclass of IonChannel describes ion channels that are not man-made, they are not engineered, they are in fact channels that are typically found/occur in nature. WildTypeCurrent This subclass of IonCurrent describes describes current measurements acquired from ion channels/ transporters, that are not man-made, they are not engineered, they are in fact ion channels or transporters that are typically found/occur in nature. WildTypeGene This subclass of Gene describes genes that are the norm in the population (not man made). WildTypeProtein This subclass of Protein describes proteins that are not man-made, they are not engineered, they are in fact proteins that are typically found/occur in nature. WildTypeSpliceVariant This subclass of SpliceVariant describes splice variants that are not man-made, they are not engineered, they are in fact variants that are typically found/occur in nature WildTypeSubunit This subclass of Subunit describes subunits that are not man-made, they are not engineered, they are in fact channels that are typically found/occur in nature. WildTypeTransporter This subclass of IonTranspoter describes ion transporters that are not man-made, they are not engineered, they are in fact transporters that are typically found/occur in nature. Zygosity http://en.wikipedia.com This subclass of Qualifier refers to the genetic condition of a zygote. In genetics, zygosity describes the similarity or dissimilarity of DNA between homologous chromosomes at a specific allelic position or gene caTransient This subclass of Observation describes the transient change in calcium-mediated light emission. rdf:List Advisors to be Named Aaron Lucas Gem Yang Raimond Winslow This purpose of this ontology is to describe electrophysiological experiments and data. This ontology was created as part of the CardioVascular Research Grid (CVRG) project which is funded through an R24 Resource from the National Heart Lung and Blood Institute (NHLBI). OWL-DL, RDF/XML-ABBREV Free, Open source Electrophysiology Ontology Second Revision