database search result Mascot dat dataset
type: Class
subclass of: database search results Mascot data
comment: This is a Mascot specific result file, produced from a database search - it is in text format. The sections of the file are delimited by a unique ID string and a Content-Type specification. [James & Satya: 03/29/05]

database search results Mascot data
type: Class
comment: A data collection that is generated by a Matrix Science Mascot database search with ms, ms-ms data
subclass of: database search output data collection

MS raw data converted format
type: Class
subclass of: ms raw data
comment: A collection of mass spectral data that has NOT been computationally processed, except that its digital format has been modified

ms raw data
type: Class
comment: A collection of mass spectral data that has NOT been computationally processed other than to change its digital format
subclass of: ms output data collection

URL parameter
type: Class
subclass of: annotation parameter
comment: A string parameter that specifies the location of a resource (such as a data file) on the internet - I.e., a Universal Resource Locator

annotation parameter
type: Class
subclass of: parameter
comment: A parameter used in the annotation of data

Bruker HCT ion trap ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

MS raw data native format
type: Class
comment: A collection of mass spectral data that has NOT been computationally processed in any way. That is, the raw output from the mass spectrometer. These may be of multiple formats [James & Satya: 03/22/05]
subclass of: ms raw data

Bruker APEX Q FT ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/27/05]

quaternary HPLC pump
type: Class
comment: A type of HPLC pump. [James & Satya: 01/31/05]
subclass of: HPLC pump

HPLC pump
type: Class
subclass of: HPLC component
comment: An HPLC component that pumps the eluant through the HPLC column, usually at high pressure and at a tightly controlled flow rate.

substance associated data collection
type: Class
subclass of: data collection
comment: a data collection that describes the physical substances such as buffers, gases etc.

data collection
type: Class
subclass of: data
equivalent class: Restriction
  on property: has data part
  min cardinality: 0
comment: This defines a broad class that includes any collection of data. It can hold other data collections, it can hold parameters, which are defined as atomic objects in ProPreO (i.e., parameters cannot be further subdivided.) [Will & Satya 02/15/06]

HPLC variable wavelength detector
type: Class
subclass of: HPLC detector
comment: A type of HPLC detector. [James & Satya: 01/31/05]

HPLC detector
type: Class
subclass of: HPLC component
comment: An HPLC instrument component that detects molecules that are eluted from the HPLC column. [James & Satya: 01/31/05]

protein accession number
type: Class
subclass of: substance accession number
comment: A parameter that specifies the unique identifier for a particular protein in a database. [Dr. York & Satya: 06/13/05]

substance accession number
type: Class
subclass of: Restriction
  on property: refers to material continuant
  all values from: chemical entity
subclass of: substance identifier
subclass of: Restriction
  all values from: string
  on property: has value
comment: A parameter that specifies the unique identifier in a database that refers to a particular molecule or gene. The name of each accession number instance should contain the accession number itself. [Dr. York & Satya: 06/13/05]

mass volume percent
type: Class
comment: A parameter describing the amount of a particular substance in a solution. The mass-volume percent of the substance is usually expressed as the number of grams of the substance divided by the number of milliliters of the solution, all divided by 100. Sometimes the mass-volume percent is abbreviated %w/v.
subclass of: component amount

component amount
type: Class
subclass of: substance amount
subclass of: Restriction
  on property: has value
  all values from: float
comment: A parameter describing the amount of a substance in a mixture. This is expressed as some sort of fractional amount, such as weight percent, molarity, etc.

Bruker microQTOF quadrupole time of flight ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

HPLC data collection
type: Class
comment: A data collection used or generated by a high performance liquid chromatography experiment
subclass of: process associated data collection

process associated data collection
type: Class
comment: A data collection that is classified according to the process that uses/creates/generates it.
subclass of: data collection

MS instrument setup parameter collection
type: Class
comment: A collection of instrumental parameters required to record mass spectral data [James & Satya: 03/27/05]
subclass of: Restriction
  all values from: MS instrumental operating parameter
  on property: has data part
subclass of: MS operating parameter collection

MS instrumental operating parameter
type: Class
subclass of: operating parameter
comment: A parameter that defines the operating state of the mass spectrometer during data collection
subclass of: MS parameter

MS operating parameter collection
type: Class
equivalent class: Class
  intersection of: operating parameter collection
  intersection of: MS data collection
comment: A collection of parameters required to perform a task that generates or processes mass spectral data
subclass of: Restriction
  all values from: Class
    union of: MS parameter
    union of: MS operating parameter collection
  on property: has data part

flourescence spectrometer
type: Class
subclass of: analytical instrument
comment: A fluorescence spectrometer measures the intensity of light that is re-emitted by a fluorescent molecule.

analytical instrument
type: Class
equivalent class: Class
  intersection of: hardware
  intersection of: Restriction
    on property: has material part
    all values from: instrument component
comment: An analytical instrument is a piece of hardware designed to measure a parameter or analyze a sample.

theoretical ion abundance
type: Class
comment: A parameter describing the theoretical abundance of a particular ion.
subclass of: ion abundance

ion abundance
type: Class
subclass of: Restriction
  on property: has value
  all values from: float
comment: A parameter describing the (measured or theoretical) abundance of a particular ion.
subclass of: ion parameter

mixture
type: Class
subclass of: Restriction
  all values from: mixture component descriptor
  on property: is described by
comment: A molecular aggregate composed of more than one type of molecule. A mixture is_described_by one or more mixture_component_descriptor(s), each of which has two parts: the component_amount and a substance_identifier that specifies the component itself.
subclass of: molecular aggregate

mixture component descriptor
type: Class
subclass of: Restriction
  on property: has data part
  some values from: substance identifier
subclass of: Restriction
  on property: has data part
  some values from: component amount
subclass of: Restriction
  cardinality: 2
  on property: has data part
comment: A pair of parameters that describes the amount of a particular component of a mixture. For example "0.5 M NaCl" describes the amount of sodium chloride in a solution - there are two parts to this description - 0.5 M specifies the amount (half molar) - NaCl identifies the component that is present at that concentration.
subclass of: substance associated data collection

is described by
type: ObjectProperty
domain: chemical entity
comment: This property describes the chemical entity in terms of either a collection of parameters (substance_associated_data_collection) or an individual parameter (substance_parameter). [Dr. York & Satya: 04/11/06]
range: Class
  union of: substance associated data collection
  union of: substance parameter

molecular aggregate
type: Class
comment: An aggregate of molecules, which may or may not be homogeneous. E.G.: a liter of water (homogeneous) a pound of wheat flour (heterogeneous) a milligram of extracted protein (heterogeneous) [will & satya 03/02/06]
subclass of: chemical entity

absolute amount
type: Class
comment: A parameter describing the amount of a substance in absolute terms (total mass, total volume, total number of moles, as appropriate). [will & satya 04/13/06]
subclass of: substance amount

substance amount
type: Class
subclass of: substance parameter
comment: A parameter describing the amount of a substance.

MS data processing parameter
type: Class
subclass of: MS parameter
comment: A parameter that is used by an application that processes mass spectral data
subclass of: data processing parameter

Turbo Sequest application
type: Class
comment: Application software developed by ThermoElectron for processing mass spectrometer data. [James & Satya: 03/27/05]
subclass of: ThermoElectron mass spectrometer data processing application

ThermoElectron mass spectrometer data processing application
type: Class
subclass of: MS data processing application
comment: Application software developed by ThermoElectron for processing mass spectrometer data. [James & Satya: 03/27/05]

operating parameter
type: Class
subclass of: parameter
comment: A parameter that is used to control the execution of a task, such as a physical parameter required for recording a mass spectrum or a computational parameter for processing a data set.

MS parameter
type: Class
subclass of: process associated parameter
comment: A parameter that is used/created/generated during the acquisition or processing of MS data [Will & Satya: 01/19/06]

database search results Spectrum Mill data
type: Class
subclass of: database search output data collection
comment: A data collection that is generated by a Spectrum Mill database search with ms, ms-ms data [James & Satya: 03/29/05]

database search output data collection
type: Class
equivalent class: Class
  intersection of: experimentally measured data collection
  intersection of: database search data collection
comment: A data collection that is generated by a database search with ms, ms-ms data [James & Satya: 03/27/05]

search and replace
type: Class
comment: A computational task involving the identification of specific data elements and their replacement by another data element.
subclass of: transform data

transform data
type: Class
subclass of: process data
comment: One of a diverse collection of computational processing tasks including: a) Changing the format b) Search and Replace (e.g., modification of DataBase) c) Sort [Dr. York & Satya: 11/21/05]

has value
type: FunctionalProperty
domain: parameter
comment: Defines the general concept of the value of a class of data. The explicit restrictions of this value (i.e., its primitive data type, cardinality, etc) are separately defined for each class in the domain. [Dr. York & Satya: 06/13/05]
type: DatatypeProperty

ion parameter
type: Class
comment: A parameter describing the properties of an ion.
subclass of: substance parameter

concentration units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of concentration

physical units
type: Class
subclass of: Restriction
  all values from: string
  on property: has value
subclass of: parameter
subclass of: Restriction
  cardinality: 0
  on property: has units
comment: A parameter defining the physical units of a parameter (measurement of setting) [will &satya 04/14/06]

PDB accession number
type: Class
comment: A parameter that specifies the unique identifier for a particular protein in the PDB database. URL: http://www.rcsb.org/pdb/ [Dr. York & Satya: 06/14/05]
subclass of: protein accession number

person
type: Class
subclass of: agent
comment: A human who initiates or implementes a task.

agent
type: Class
comment: An agent is a real world object that causes something to happen, i.e., it initiates or implements a process. Examples are human operators, analytical instruments, enzymes, and software applications
subclass of: material continuant

potential units
type: Class
comment: A parameter defining the physical units of potential, such as electrical potential, gravitational potential, etc. Potentials generally have units "energy per amount", for example volts are Joules per Coulomb
subclass of: physical units

xml ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection (in XML format) consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment.

ms-ms peak list
type: Class
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. Often, the abundance of the ion is included in the peak list. The ms/ms peak list can be used to perform database searching or denovo sequencing. [James & Satya: 03/27/05]
subclass of: ms processed data

MS source cone voltage
type: Class
equivalent class: Restriction
  all values from: float
  on property: has value
comment: A parameter that defines the voltage applied to the inlet cone. [James & Satya: 02/24/05]
subclass of: Restriction
  all values from: electrical potential units
  on property: has units
subclass of: MS source ESI parameter

electrical potential units
type: Class
subclass of: potential units
comment: A parameter describing the units of electrical potential

MS source ESI parameter
type: Class
comment: A parameter associated with an electrospray ionization source.
subclass of: MS source parameter

Sciex API III ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. Peak lists exported from PE Sciex API III contain data from a single MS/MS spectrum. Since the file format does not include details of the precursor peptide m/z, this information must be entered manually into the PRECURSOR and CHARGE form fields. This limitation also means that multiple spectra cannot be merged into a single data file. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05]

Masslynx proteinlynx denovo sequencing results data
type: Class
subclass of: denovo sequencing output data collection
comment: A data collection produced by performing Proteinlynx denovo sequecing. [James & Satya: 03/29/05]

denovo sequencing output data collection
type: Class
comment: A data collection generated by a denovo sequencing process with ms-ms data. [James & Satya: 03/27/05]
equivalent class: Class
  intersection of: denovo sequencing data collection
  intersection of: experimentally measured data collection

Agilent HPLC
type: Class
comment: A High Performance Liquid Chromatograph manufactured by Agilent Technologies. [James & Satya: 01/31/05]
subclass of: high performance liquid chromatograph

high performance liquid chromatograph
type: Class
subclass of: Restriction
  on property: has material part
  all values from: HPLC component
comment: An instrument that separates molecules by passing a solution of the molecules through a column containing a solid matrix that differentially interacts with the molecules.
subclass of: analytical instrument

tranform representation format
type: Class
subclass of: transform data format
comment: The transformation of the representational format of data. For example, FASTA format to GCG format. [Dr. York & Satya: 11/21/05]

transform data format
type: Class
comment: The task of transforming the format of data, usually creating a new data file with either new file format or data encoding. [Dr. York & Satya: 11/21/05]
subclass of: transform data

Micromass MALDI micro MX MALDI TOF ms raw data
type: Class
comment: The raw data output from this intrument. [James & Satya: 03/22/05]
subclass of: MS raw data native format

Proteinlynx micromass MALDI data processing parameters collection
type: Class
comment: The collection of processing parameters used by Proteinlynx when converting a MALDI '.raw' file into a '.pkl' or a '.dta' file, when using Proteinlynx. [James & Satya: 04/01/05]
subclass of: MS data processing parameter collection

Proteinlynx micromass electrospray data processing parameters collection
type: Class
subclass of: MS data processing parameter collection
comment: The collection of processing parameters used by Proteinlynx when converting a electrospray '.raw' file into a '.pkl' or a '.dta' file, when using Proteinlynx. [James & Satya: 04/01/05]

triple quadrupole mass spectrometer
type: Class
comment: A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]
subclass of: tandem mass spectrometer

tandem mass spectrometer
type: Class
subclass of: mass spectrometer
comment: A mass spectrometer that can perform both MS and MS/MS analysis. [James & Satya: 03/27/05]

HPLC autosampler
type: Class
comment: An HPLC component that is programmed to automatically inject samples into the HPLC column. [James & Satya: 01/31/05]
subclass of: HPLC component

HPLC component
type: Class
comment: A component of a hgh-performance liquid chromatograph
subclass of: instrument component

annotation associated data collection
type: Class
subclass of: data collection
comment: a data collection that is used to annotate other data

transform glycan structure format
type: Class
comment: This describes the task of transforming a given glycan structure from one representation format into another. For example from LINUCS to GLYDE. [Dr. York & Satya: 11/21/05]
subclass of: tranform representation format

solution
type: Class
subclass of: mixture
comment: A mixture in the form of a homogeneous liquid contaning a solvent and at least one solute. A "solution" is_described_by one or more mixture_component_descriptor(s), each of which has two parts: the component_amount and a substance_identifier that specifies the identity of the component. This is a flexible way of describing solutions. For example, a solution can be described as a mixture of two other solutions (e.g., buffer A and buffer B), in which case the mixture_component_descriptor(s) each specify the identity and amount of each of these buffers. Alternatively, a solution can be described according to the concentrations of its solutes (dissolved molecules), each of which is specified by a mixture_component_descriptor. In this case, complete description of the solution requires that the solvent be specified using the property has_solvent, which points to an instance of the class "solvent". [Satya & Will 03/02/06]

MS source MALDI laser intensity
type: Class
subclass of: MS source MALDI parameter
subclass of: Restriction
  on property: has units
  all values from: laser pulse intensity units
comment: A parameter that defines the intensity of the laser used in the MS experiment. [James & Satya: 02/24/05]
equivalent class: Restriction
  on property: has value
  all values from: float

MS source MALDI parameter
type: Class
comment: A parameter associated with a matrix assisted laser induced ionization source. [James & Satya: 02/24/05]
subclass of: MS source parameter

laser pulse intensity units
type: Class
comment: A parameter that defines the units used to describe the intensity of a laser pulse
subclass of: physical units

absolute volume
type: Class
subclass of: absolute amount
comment: A parameter describing the total volume of a particular substance (e.g., 5 Liters of water) in a molecular aggregate

small organic molecule
type: Class
subclass of: small molecule
comment: A small molecule that contains the element carbon.

small molecule
type: Class
comment: A molecule that is very generally classified by its small size. This class is intended to allow the classification of molecules that are encountered in proteomics analysis (such as a solvent molecule or a MALDI matrix component), but are not classified as a major type of biomolecule.
subclass of: molecule

data
type: Class
comment: Data constitute the basic units of information. Data can include collections of information or individual units of information. Data can be experimental (measured) or theoretical (calculated). [satya 02/15/06]

MS source parameter
type: Class
comment: A parameter that defines the operating state of the mass spectrometer ion source during data collection [Will & Satya 02/15/06]
subclass of: MS instrumental operating parameter

MS source parameter collection
type: Class
subclass of: MS instrument setup parameter collection
subclass of: Restriction
  all values from: MS source parameter
  on property: has data part
comment: A collection of parameters controlling the operation of the ion source of a mass spectrometer [James & Satya: 02/24/05]

Masslynx Micromass application
type: Class
comment: Application software developed by Micromass for processing mass spectrometer data. [James & Satya: 03/27/05]
subclass of: Micromass mass spectrometer data processing application

Micromass mass spectrometer data processing application
type: Class
comment: Application software developed by Micromass for processing mass spectrometer data. [James & Satya: 03/27/05]
subclass of: MS data processing application

lectin affinity HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

HPLC column
type: Class
subclass of: HPLC component
comment: A matrix-containing tube that is used for high-performance liquid chromatography. The sample is separated into its components by injecting it into the column and elutimng with a solvent or buffer.

tryptic peptide
type: Class
subclass of: Restriction
  all values from: trypsin
  on property: generated by proteolytic enzyme
comment: A peptide that is generated by treatment of a protein with the proteolytic enzyme trypsin . [Dr. York & Satya: 06/28/05]
subclass of: peptide

trypsin
type: Class
subclass of: proteolytic enzyme
comment: Class of related proteolytic enzymes that cleave after basic amino acids K & R except when followed by P. [Dr. York & Satya: 06/28/05]

generated by proteolytic enzyme
type: ObjectProperty
range: proteolytic enzyme
comment: associates the peptide with the enzyme that released it. [Dr. York & Satya: 06/28/05]
sub property of: is effect of
domain: peptide

peptide
type: Class
subclass of: molecule
subclass of: Restriction
  all values from: Class
    complement of: Class
      union of: DNA nucleotide sequence
      union of: RNA nucleotide sequence
  on property: is described by
subclass of: Restriction
  all values from: Class
    complement of: polynucleotide accession number
  on property: is described by
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: glycan accession number
comment: A biomolecule composed of amino acids connected by amide bonds. A peptide can be generated by fragmentation of a protein by a protease (e.g. trypsin). In ProPreO, peptides are distinguished from proteins mainly by size (oligopeptides are smaller, and thereby distinct from polypeptides). [Dr. York & Satya: 06/10/05]

organism
type: Class
comment: A biological species, such as Homo sapiens or Arabidopsis thaliana. The taxonomic classification of a biological species are modeled in other ontologies. http://obo.sourceforge.net/cgi-bin/detail.cgi?ncbi_taxonomy http://obo.sourceforge.net/cgi-bin/detail.cgi?newt Instances of specific organisms may be specified iwithin ProPreO, but their complete systematic taxonomy should be found in these other ontologies. [Dr. York & Satya: 06/28/05]
subclass of: biological continuant

biological continuant
type: Class
subclass of: material continuant
comment: This class includes organisms at various stages of development or life-cycle (e.g., spore, seed, blastula, embryo, adult, epimastigote) and parts of these organisms (e.g., organs, tissues and cells). It also includes cultured cells and tissues (e.g., cultured embryonic stem cells). The ProPreO is not meant to explicitly describe all of these objects. Rather, it is meant to provide access to ontological descriptions of these objects by defining broad classes that are more fully modeled in other ontologies.

CHEBI ID
type: Class
subclass of: substance accession number
comment: A parameter that corresponds to the CHEBI ID from the ChEBI Ontology http://www.ebi.ac.uk/chebi/

experimentally measured parameter
type: Class
subclass of: parameter
comment: An experimentally measured parameter, either raw or processed. (E.G., signal intensity) A collection of such parameters can serve as the input to a data processing task or the output of an experimental measurement or computational task.

parameter
type: Class
subclass of: data
comment: In ProPreO, a parameter is a single, indivisible datum (i.e., parameters cannot be further subdivided.) Collections of parameters are called data_collections in ProPreO. Note that in ProPreO, a parameter (such as a substance_identifier or biological_source_parameter) may refer to a specific object (such as an organism or a molecule), but the parameter and the object that it refers to are separate. In these cases, the parameter is piece of information that may be found, for example, in a data file and the object it points to is a real world object of class of objects. These two entities are related by the property "refers_to_material_continuant". [satya 02/15/06]
equivalent class: Restriction
  on property: has data part
  cardinality: 0

transform peptide sequence format
type: Class
comment: This describes the tranformation of a given peptide sequence from one format into another. [Dr. York & Satya: 11/21/05]
subclass of: tranform representation format

procaryotic organism
type: Class
comment: An organism whose cells do not have a nucleus or internal membranes. [Dr. York & Satya: 06/28/05]
subclass of: organism

source organism
type: Class
comment: A parameter that specifies the organism from which the biological sample is taken.
subclass of: Restriction
  all values from: organism
  on property: refers to material continuant
subclass of: biological source parameter

refers to material continuant
type: FunctionalProperty
domain: parameter
comment: A parameter may describe a chemical entity such as a HPLC solvent or a MALDI matrix. This property relates such a parameterto a specific chemical entity which is not a parameter but a continuant. [will & satya 04/10/06]
type: ObjectProperty
range: material continuant

biological source parameter
type: Class
subclass of: parameter
comment: A parameter that describes some aspect of part of an organism that was used as the source of a biological_sample or biomolecule. A biological source parameter refers to, for example, a species, organ, cell type, life-cycle stage, develomental stage, etc. Within the context of ProPreO, biological source parameters are meant to describe laboratory samples that are analyzed by or used in proteomics or glycoproteomics methods.
subclass of: Restriction
  on property: refers to material continuant
  all values from: biological continuant

LINUCS ID
type: Class
comment: A parameter that specifies the unique glycan identifier in SWEETDB. URL: http://www.glycosciences.de/sweetdb/index.php [Dr. York & Satya: 06/13/05]
subclass of: glycan accession number

glycan accession number
type: Class
comment: A parameter that specifies the unique identifierfor a glycan. [Dr. York & Satya: 06/13/05]
subclass of: substance accession number

MS data collection
type: Class
subclass of: process associated data collection
comment: A data collection used or generated by a mass spectrometry experiment

HPLC chromatogram
type: Class
comment: A data collection (chromatogram) generated by an HPLC experiment -This typically consists of a collection of time/signal intensity pairs [James & Satya: 03/29/05]
equivalent class: Restriction
  all values from: HPLC time signal pair
  on property: has data part
subclass of: HPLC experimental data collection

HPLC time signal pair
type: Class
comment: A single time-point generated by an HPLC experiment - This corresponds to a pair of parameters, the internal HPLC time and the detector signal at that time.
subclass of: HPLC experimental data collection
equivalent class: Class
  intersection of: Restriction
    some values from: HPLC time parameter
    on property: has data part
  intersection of: Restriction
    some values from: HPLC detector signal
    on property: has data part

HPLC experimental data collection
type: Class
comment: c
equivalent class: Class
  intersection of: experimentally measured data collection
  intersection of: HPLC data collection

Finnigan ASC ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. Files in this format are created by the LIST command on the ICIS data system. The header block for each MS/MS dataset begins with a "LIST:" field. The text in this field is used by Mascot to identify the query, equivalent to an embedded TITLE parameter. The ASC file header does not specify a charge state for the precursor peptide. This can be specified (globally) on the search form, or by an embedded CHARGE parameter at the head of the data file. The precursor peptide m/z value is parsed from the "Mode:" field. Mascot uses the prevailing CHARGE value to calculate Mr from the observed m/z. A blank line to delimit MS/MS datasets is optional. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05]

reversed-phase HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

Bruker ultraflex TOF TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

operating parameter collection
type: Class
subclass of: data collection
comment: A data collection that is used to control the execution of a task, such as the physical parameters required for recording a mass spectrum or the computational parameters for processing a data set.

Bruker HCT ion trap mass spectrometer
type: Class
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: ion trap mass spectrometer
subclass of: Restriction
  all values from: Bruker HCT ion trap ms raw data
  on property: generates raw data

ion trap mass spectrometer
type: Class
comment: A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]
subclass of: tandem mass spectrometer

instrument component
type: Class
comment: A part of a scientific instrument. Many instruments are modular, assembled by combining several interacting components.
subclass of: hardware

hardware
type: Class
comment: An object manufactured to perform a specfic task. Examples are bolts (which hold other objects together), computers (which execute software), and mass spectrometers (which separate and count ions based on their mass to charge ratios).
subclass of: agent

HPLC micro well plate autosampler
type: Class
comment: A type of HPLC autosampler. [James & Satya: 01/31/05]
subclass of: HPLC autosampler

data processing parameter
type: Class
subclass of: operating parameter
comment: A parameter that is used by a data processing application

SemURI parameter
type: Class
subclass of: annotation parameter
comment: By semantic URI (SemURI) we mean an URI that lexically incorporates semantic description by succinctly representing a chronologically ordered list of concepts that are defined in ProPreO or other ontologies. These concepts can include both (physical and computational) tasks and the (physical and digital) objects that these tasks use and generate. Thus, each task or object class is assigned a SemURI_concept_ID, which is appended (along with a SemURI_instance_ID) to the SemURI of the the object's predecessor to generate a new SemURI that identifies the new task or object. Thus, the SemURI constitutes a very succinct representation of the entire provenance of an object, including all of the tasks and intermediate objects in its history.

simulate ms data
type: Class
comment: Tthe simulation of mass spectra. For example, calculation of an isotopic distribution based on elemental composition and subsequent simulation of a mass spectum based on the calculated isotopic distribution. [Dr. York & Satya: 11/21/05]
subclass of: simulate analytical data
subclass of: Restriction
  on property: has input data
  all values from: Class
    union of: mass
    union of: molecular sequence
    union of: elemental composition

simulate analytical data
type: Class
subclass of: simulate data
comment: The simulation of the output of an analytical instrument like NMR, ms or chromatography. It is computed based on a set of input parametres. [Dr. York & Satya: 11/21/05]

has input data
type: ObjectProperty
domain: task
comment: This object property is subsumed by "has_participant" object property as defined in Barry Smith et. al. "Relations in biomedical ontologies", Genome Biology, Vol 6, Article R46.
sub property of: has participant
range: data collection

mass
type: Class
subclass of: Restriction
  all values from: float
  on property: has value
subclass of: ion parameter
subclass of: molecular parameter
subclass of: Restriction
  cardinality: 1
  on property: has value
comment: Describes the molecular mass of a molecule or ion . [Dr. York & Satya: 06/13/05]

molecular sequence
type: Class
subclass of: molecular parameter
comment: A parameter describing the sequence of residues in a biopolymer. [Dr. York & Satya: 06/28/05]

elemental composition
type: Class
comment: A parameter describing the identities of chemical elements and the number of atoms of each element that constitute a molecule. [Dr. York & Satya: 11/21/05]
subclass of: Restriction
  cardinality: 0
  on property: has units
subclass of: molecular parameter

ms processed data
type: Class
comment: A collection of mass spectral data that has been computationally processed - E.G. a peak list [James & Satya: 03/22/05]
subclass of: ms output data collection

ABI 4700 TOF TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this instrument. [James & Satya: 03/22/05]

HPLC excitation wavelength
type: Class
comment: A parameter that describes the excitation wavelength of a fluorescence HPLC detector. [James & Satya: 01/31/05]
subclass of: Restriction
  on property: has value
  all values from: float
subclass of: Restriction
  all values from: length units
  on property: has units
subclass of: HPLC instrumental operating parameter

length units
type: Class
comment: A parameter defining the physical units of length
subclass of: physical units

HPLC instrumental operating parameter
type: Class
subclass of: operating parameter
comment: A parameter that defines the operating state of the chromatograph during data collection
subclass of: HPLC parameter

Bruker APEX Q FT mass spectrometer
type: Class
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: hybrid tandem mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker APEX Q FT ms raw data

hybrid tandem mass spectrometer
type: Class
subclass of: tandem mass spectrometer
comment: A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]

HPLC refractive index detector
type: Class
comment: A type of HPLC detector. [James & Satya: 01/31/05]
subclass of: HPLC detector

Bruker APEX IV ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this instrument. [James & Satya: 03/27/05]

Micromass QTOF 2 quadrupole time of flight ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

PEAKS denovo sequencing results data
type: Class
comment: A data collection produced by performing PEAKKS denovo sequecing. [James & Satya: 03/29/05]
subclass of: denovo sequencing output data collection

Bruker APEX IV mass spectrometer
type: Class
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: fourier transform mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker APEX IV ms raw data

fourier transform mass spectrometer
type: Class
subclass of: tandem mass spectrometer
comment: The type of tandem_mass_spectrometer. [James & Satya: 03/27/05]

volume units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of time

ESI source
type: Class
comment: For for > microlitre/min flow rates. [James & Satya: 02/24/05]
subclass of: MS source

HPLC multiwavelength detector
type: Class
comment: A type of HPLC detector. [James & Satya: 01/31/05]
subclass of: HPLC detector

MS source ESI capillary voltage
type: Class
subclass of: Restriction
  on property: has units
  all values from: electrical potential units
comment: A parameter that defines the voltage applied to the ESI capillary. [James & Satya: 02/24/05]
subclass of: MS source ESI parameter
equivalent class: Restriction
  all values from: float
  on property: has value

theoretical isoelectric point
type: Class
subclass of: isoelectric point
comment: Calculated from the molecular structure. [Dr. York & Satya: 06/28/05]

isoelectric point
type: Class
comment: Describes the pH at which a zwitter ionic molecule has no charge also called pI. [Dr. York & Satya: 06/28/05]
subclass of: molecular parameter

HPLC microscale fraction collector
type: Class
subclass of: HPLC fraction collector
comment: An HPLC fraction collector that directs the eluant from an microscale HPLC experiment. [James & Satya: 01/31/05]

HPLC fraction collector
type: Class
subclass of: HPLC component
comment: An HPLC instrument component that directs the eluant from the HPLC column to a series of separate vessels (tubes of wells). The collector may direct the eluant to different vessels based on elution time, detector response, or some other criterion.

MS analyzer scan time
type: Class
comment: A parameter that defines the length of time for an MS or MS-MS scan. [James & Satya: 02/24/05]
subclass of: MS analyzer parameter

MS analyzer parameter
type: Class
subclass of: MS instrumental operating parameter
comment: A parameter that defines the operating state of the mass spectrometer analyzer during data collection [Will & Satya 02/15/06]

antibody affinity HPLC column
type: Class
comment: A type of HPLC column
subclass of: HPLC column

cell
type: Class
comment: A cell, such as a neutrophil or a stem cell. These are more fully modeled in the cell ontology http://obo.sourceforge.net/cgi-bin/detail.cgi?cell
subclass of: biological continuant

simulate data
type: Class
subclass of: computational task
comment: The simulation of data from input data. For example, simulation of a theoretical spectrum from a chemical composition. [Dr. York & Satya: 11/21/05]

source cell
type: Class
comment: A parameter that specifies the cell type from which the biological sample is taken.
subclass of: biological source parameter
subclass of: Restriction
  on property: refers to material continuant
  all values from: cell

ABI Voyager DE Pro MALDI TOF mass spectrometer
type: Class
subclass of: Restriction
  all values from: ABI Voyager DE Pro MALDI TOF ms raw data
  on property: generates raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]
subclass of: MALDI-TOF mass spectrometer

ABI Voyager DE Pro MALDI TOF ms raw data
type: Class
comment: The raw data output from this instrument. [James & Satya: 03/22/05]
subclass of: MS raw data native format

MALDI-TOF mass spectrometer
type: Class
subclass of: mass spectrometer
subclass of: Restriction
  on property: has material part
  all values from: Class
    union of: TOF analyzer
    union of: MALDI source
    union of: MS detector
comment: A Matrix-Assisted-Laser-Desorption-Time-of-Flight mass spectrometer. Such a spectrometer contains a MALDI source and a TOF analyzer. [James & Satya: 03/27/05]

solid mixture
type: Class
subclass of: mixture
comment: A mixture that is in the solid state, for example, dry baking powder, composed of solid NaHCO3 and tartaric acid. [Satya & Will 03/02/06]

HPLC parameter
type: Class
subclass of: process associated parameter
comment: A parameter that is used/created/generated during the acquisition or processing of HPLC data

process associated parameter
type: Class
subclass of: parameter
comment: A parameter that is classified according to the process that uses/creates/generates it. [will & satya 02/17/06]

MS component
type: Class
subclass of: instrument component
comment: A component of a mass spectrometer

Bruker HCTplus ion trap mass spectrometer
type: Class
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker HCTplus ion trap ms raw data
subclass of: ion trap mass spectrometer
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker HCTplus ion trap ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

MS source MALDI number of laser shots
type: Class
subclass of: MS source MALDI parameter
comment: A parameter that defines the number of laser shots in a MALDI experiment. This is a pure integer (no units). [James & Satya: 02/24/05]
equivalent class: Restriction
  all values from: int
  on property: has value
subclass of: Restriction
  on property: has units
  cardinality: 0

raw2mzXML transformation
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has SemURI concept ID
    has value: raw2mzXML transformation tsuka
  intersection of: Restriction
    all values from: mzXML ms raw data
    on property: has output data
  intersection of: Restriction
    all values from: ms raw data
    on property: has input experimental data collection
comment: This task converts a raw mass spec data file into the mzXML format.
subclass of: tranform encoding format

has SemURI concept ID
type: ObjectProperty
range: SemURI concept ID
domain: Class
  union of: data
  union of: task
  union of: material continuant
type: InverseFunctionalProperty
type: FunctionalProperty
sub property of: has provenance property
comment: This property enables mapping of each concept in ProPreO to a concept in the SemURI framework. [will & satya 03/03/06]

mzXML ms raw data
type: Class
comment: A collection of mass spectral data that has NOT been computationally processed, except that it has been converted to mzXML format
equivalent class: Restriction
  on property: has SemURI concept ID
  has value: mzXML ms raw data tsuka
subclass of: MS raw data converted format

has output data
type: ObjectProperty
sub property of: is cause of
range: experimentally measured data collection
comment: This object property is subsumed by "has_participant" object property as defined in Barry Smith et. al. "Relations in biomedical ontologies", Genome Biology, Vol 6, Article R46.
domain: Class
  union of: task
  union of: analytical instrument

tranform encoding format
type: Class
subclass of: transform data format
comment: The task of transforming one encoding type into another. For example, binary to ascii. [Dr. York & Satya: 11/21/05]

process data
type: Class
comment: The task of processing data using computational applications. [Dr. York & Satya: 11/21/05]
subclass of: computational task

ms output data collection
type: Class
equivalent class: Class
  intersection of: experimentally measured data collection
  intersection of: MS data collection
comment: A data collection generated by a mass spectrometer or mass spectral data processing application

experimentally measured data collection
type: Class
subclass of: data collection
comment: This describes collections of experimental (measured) data, either raw or processed. Such data can serve as the input to a data processing task or the output of an experimental measurement or computational task.

capillary HPLC pump
type: Class
comment: A type of HPLC pump. [James & Satya: 01/31/05]
subclass of: HPLC pump

solvent
type: Class
subclass of: pure substance
comment: The solvent of a solution, consisting of many copies of the solvent molecule.

pure substance
type: Class
subclass of: Restriction
  all values from: molecule
  on property: has material part
subclass of: molecular aggregate
comment: A molecular aggregate composed of many copies of same molecule. [will & satya 03/02/06]

theoretical ion charge
type: Class
subclass of: ion charge
comment: A parameter describing the theoretical charge of a particular ion.

ion charge
type: Class
subclass of: Restriction
  on property: has value
  all values from: int
subclass of: ion parameter
subclass of: Restriction
  on property: has units
  all values from: electrical charge units
comment: A parameter describing the (measured or theoretical) charge of a particular ion.

Bruker esquire4000 ion trap mass spectrometer
type: Class
subclass of: ion trap mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker esquire4000 ion trap ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker esquire4000 ion trap ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

sort data
type: Class
subclass of: transform data
comment: A computational task involving the reordering of data elements according to a specific set of criteria.

experimental isoelectric point
type: Class
comment: Measured from an experiment. [Dr. York & Satya: 06/28/05]
subclass of: isoelectric point

MS detector
type: Class
subclass of: MS component
comment: This is for self-manufactured or modified that are not found under the mass spectrometer instruments. [James & Satya: 02/24/05]

record ms data
type: Class
subclass of: record raw data
comment: Tthe physical task of running a mass spectrometer on a specific sample and recording the resulting spectra. [Dr. York & Satya: 11/21/05]
subclass of: Restriction
  all values from: MS raw data native format
  on property: generates raw data

record raw data
type: Class
subclass of: physical task
comment: The task of recording raw data using an analytical instrument. [Dr. York & Satya: 11/21/05]

strong cation exchange HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

substance parameter
type: Class
subclass of: parameter
comment: A parameter that describes a physical substance such as a buffer, gas etc.

REFSEQ polynucleotide accession number
type: Class
comment: A parameter that specifies the unique identifier that refers to a particular gene or other nucleotide sequence in the RefSeq system. URL: www.ncbi.nlm.nih.gov/RefSeq/key.html [Dr. York & Satya: 06/23/05]
subclass of: polynucleotide accession number

polynucleotide accession number
type: Class
comment: A parameter that specifies the unique identifier in a database that refers to a particular gene or other nucleotide sequence. [Dr. York & Satya: 06/24/05]
subclass of: substance accession number

SemURI
type: Class
comment: The semantic Universal Resource Identifier (semURI) for a specific instance defined in ProPreO or other aligned ontology. By semantic URI we mean an URI that lexically incorporates semantic description by succinctly representing a chronologically ordered list of concepts that are defined in ProPreO or other ontologies. These concepts can include both (physical and computational) tasks and the (physical and digital) objects that these tasks use and generate. Thus, each task or object class is assigned a SemURI_concept_ID, which is appended (along with a SemURI_instance_ID) to the SemURI of the the object's predecessor to generate a new SemURI that identifies the new task or object. Thus, the SemURI constitutes a very succinct representation of the entire provenance of an object, including all of the tasks and intermediate objects in its history.
subclass of: SemURI parameter
subclass of: Restriction
  all values from: string
  on property: has value

chemical agent
type: Class
subclass of: agent
comment: A chemical agent is a chemical or molecule (such as an enzyme) that implements or initiates a molecular process.

molecule
type: Class
subclass of: chemical entity
comment: An individual molecule, categorized according to a few broadly defined classes. [Dr. York & Satya: 06/10/05]
subclass of: Restriction
  on property: is described by
  all values from: Class
    union of: molecular parameter
    union of: substance accession number
equivalent class: Restriction
  on property: material part of
  all values from: molecular aggregate

REFSEQ protein accession number
type: Class
subclass of: protein accession number
comment: A parameter that specifies the unique identifier for a particular protein in the RefSeq system. URL: www.ncbi.nlm.nih.gov/RefSeq/ [Dr. York & Satya: 06/14/05]

life-cycle form
type: Class
subclass of: biological continuant
comment: An organism in the form it adopts at a specific stage in its life-cycle. For example, an epimastigote is a life-cycle form of a Trypanosome. Ontologies that more fully model life-cycle stages are in development, for example, http://obo.sourceforge.net/cgi-bin/detail.cgi?plasmodium_life_cycle

HPLC buffer
type: Class
subclass of: HPLC instrumental operating parameter
comment: A parameter that identifies the elution buffer used in HPLC. A mixture of buffers is often prepared in a mixing device to form a time-dependent elution gradient. The HPLC_buffer parameter is a substance identifier, which points to an instance of "solution". A "solution" is_described_by one or more mixture_component_descriptor(s), each of which has two parts: the component_amount and a substance_identifier that specifies the identity of the component. This is a flexible way of describing solutions. For example, a solution can be described as a mixture of two other solutions (e.g., buffer A and buffer B), in which case the mixture_component_descriptor(s) each specify the identity and amount of each of these buffers. Alternatively, a solution can be described according to the concentrations of its solutes (molecules), each of which is specified by a mixture_component_descriptor. In this case, complete description of the solution requires that the solvent be specified using the property has_solvent, which points to an instance of the class "solvent". [James & Satya: 01/31/05]
subclass of: Restriction
  on property: has units
  cardinality: 0
subclass of: Restriction
  on property: refers to material continuant
  all values from: Class
    union of: solution
    union of: solvent
subclass of: substance identifier

substance identifier
type: Class
subclass of: substance parameter
comment: A parameter that identifies a molecule or molecular aggergate.

Finnigan LTQ FT ms raw data
type: Class
comment: The raw data output from this intrument. [James & Satya: 03/27/05]
subclass of: MS raw data native format

proteolytic enzyme
type: Class
comment: A protein that catalyzes the cleavage of peptide bonds in proteins to generate peptides. [Dr. York & Satya: 06/28/05]
subclass of: enzyme

enzyme
type: Class
comment: An enzyme is a protein or protein complex that catalyzes a specific set of chemical reactions.
subclass of: chemical agent
subclass of: polypeptide

Micromass Quatro premier triple quadrupole mass spectrometer
type: Class
subclass of: Restriction
  on property: generates raw data
  all values from: Micromass Quatro premier triple quadrupole ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: triple quadrupole mass spectrometer

Micromass Quatro premier triple quadrupole ms raw data
type: Class
comment: The raw data output from this intrument. [James & Satya: 03/22/05]
subclass of: MS raw data native format

Micromass Q TOF micro quadrupole time of flight ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Applied Bio Systems mass spectrometer data processing application
type: Class
comment: Application software developed by Applied Bio Systems for processing mass spectrometer data. [James & Satya: 03/27/05]
subclass of: MS data processing application

MS data processing application
type: Class
subclass of: data processing application
comment: Application software used in processing/manipulating ms or ms-ms data. [James & Satya: 03/27/05]

quadrupole analyzer
type: Class
subclass of: MS analyzer
comment: A type of MS analyzer

MS analyzer
type: Class
subclass of: MS component
comment: A mass spectromete component that separates ions according to their mass to charge ratio. Ions are produced in the ion source.

bacteria
type: Class
comment: A diverse group of prokaryotic organisms, distinct from the Archaea.
subclass of: procaryotic organism

MS data processing parameter collection
type: Class
comment: A collection of computational parameters required to process ms or ms-ms data [James & Satya: 03/27/05]
subclass of: MS operating parameter collection

experimental ion abundance
type: Class
comment: A parameter describing the measured abundance of a particular ion.
subclass of: MS experimentally measured parameter
subclass of: ion abundance

MS experimentally measured parameter
type: Class
subclass of: MS parameter
comment: A parameter that is measured during an MS experiment - E.G. the abundance of an ion having a particular m/z value.
subclass of: experimentally measured parameter

denovo sequencing data collection
type: Class
subclass of: process associated data collection
comment: A data collection used or generated by a denovo sequencing process with ms-ms data.

Nano ESI source
type: Class
subclass of: ESI source
comment: Electrospray source for flow rates < 3 microlitres/min. [James & Satya: 02/24/05]

Bruker autoflex TOF TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

parent ion
type: Class
subclass of: ion
comment: An ion, generated in a mass spectrometer, that is subsequently dissociated into fragment ions in an MS/MS experiment

ion
type: Class
comment: An electrically charged chemical species, which may be a single atom (e.g., Na+), or many atoms (e.g., NH4+).
subclass of: Restriction
  on property: is described by
  all values from: ion parameter
subclass of: chemical entity

experimental ion charge
type: Class
subclass of: MS experimentally measured parameter
subclass of: ion charge
comment: A parameter describing the measured charge of a particular ion.

ABI 4700 TOF TOF mass spectrometer
type: Class
subclass of: tandem time of flight mass spectrometer
comment: Defines type of tandem mass spectrometer. Tandem time-of-flight spectrometer can perform ms and ms/ms type of analysis. [James & Satya: 01/31/05]
subclass of: Restriction
  on property: generates raw data
  all values from: ABI 4700 TOF TOF ms raw data

tandem time of flight mass spectrometer
type: Class
comment: A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]
subclass of: tandem mass spectrometer

molecular parameter
type: Class
subclass of: substance parameter
comment: A parameter describing the identity or a physical property of a molecule. [James & Satya: 04/01/05]

binary HPLC pump
type: Class
comment: A type of HPLC pump. [James & Satya: 01/31/05]
subclass of: HPLC pump

molecular description
type: Class
subclass of: Restriction
  all values from: string
  on property: has value
subclass of: molecular parameter
subclass of: Restriction
  on property: has value
  cardinality: 1
comment: Describes the molecule, its properties, origin etc. [Dr. York & Satya: 06/13/05]

chemical entity
type: Class
subclass of: material continuant
comment: A material continuant that is described chiefly with respect to its chemical composition.

material continuant
type: Class
comment: A material continuant is a real-world object.

Bruker ultraflex TOF TOF mass spectrometer
type: Class
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker ultraflex TOF TOF ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: tandem time of flight mass spectrometer

simulate molecular data
type: Class
comment: The computational simulation of the structure, physical properties or behavior of a molecule, such as conformational trajectory or reaction kinetics. [Dr. York & Satya: 11/21/05]
subclass of: simulate data

Bruker autoflex MALDI TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

HPLC operating parameter collection
type: Class
subclass of: Restriction
  on property: has data part
  all values from: Class
    union of: HPLC parameter
    union of: HPLC gradient program
    union of: HPLC gradient time point
equivalent class: Class
  intersection of: operating parameter collection
  intersection of: HPLC data collection
comment: A collection of parameters required to perform or analyze an HPLC run. [Dr. York & Satya: 05/17/05]

HPLC gradient program
type: Class
subclass of: Restriction
  all values from: HPLC gradient time point
  on property: has data part
comment: A collection of parameters that describe the solvent gradient for an HPLC run [Dr. York & Satya: 05/17/05]
subclass of: HPLC operating parameter collection

HPLC gradient time point
type: Class
subclass of: HPLC operating parameter collection
comment: A collection of parameters that defines a HPLC run time and the associated buffer mixture that comprises the eluent at that time. It can have multiple values of component portion for that time value. [Dr. York & Satya: 06/28/05]
equivalent class: Class
  intersection of: Restriction
    some values from: HPLC time parameter
    on property: has data part
  intersection of: Restriction
    on property: has data part
    some values from: mixture component descriptor

glycan
type: Class
subclass of: Restriction
  all values from: Class
    complement of: polynucleotide accession number
  on property: is described by
comment: A biomolecule composed of glycosyl residues. A glycan is a type of carbohydrate molecule. [Dr. York & Satya: 06/10/05]
subclass of: Restriction
  all values from: Class
    complement of: protein accession number
  on property: is described by
subclass of: Restriction
  all values from: Class
    complement of: molecular sequence
  on property: is described by
subclass of: molecule

magnetic sector analyzer
type: Class
subclass of: MS analyzer
comment: A type of MS analyzer

mole fraction
type: Class
subclass of: component amount
comment: A parameter describing the amount of a substance in a solution. The mole fraction is the number of moles of a particular solute divided by the total number of moles of in the solution.

computational task
type: Class
comment: A task involved in the processing of data by a computational application. [Dr. York & Satya: 11/21/05]
subclass of: task

task
type: Class
comment: A process that is initiated or implemented by an agent.

molarity
type: Class
comment: A parameter describing the amount of a substance in a solution. The molarity is the number of moles of the substance that is dissolved in one Liter of the solution.
subclass of: component amount

HPLC diode array detector
type: Class
subclass of: HPLC detector
comment: A type of HPLC detector. [James & Satya: 01/31/05]

HPLC fluorenscence detector
type: Class
subclass of: HPLC detector
comment: A type of HPLC detector. [James & Satya: 01/31/05]

RNA nucleotide sequence
type: Class
comment: A parameter describing the sequence of nucleotides in an RNA molecule. Nucleotides are listed from the 5' end to the 3' end.
subclass of: molecular sequence

identify components
type: Class
subclass of: hybrid task
comment: The complex task of identifhying the components of a mixture. This may involve, for example, HPLC of the mixture (i.e. separate_by_HPLC) followed by computational peak picking and peak matching (i.e., classify_data).

hybrid task
type: Class
comment: A task that combines both physical and computational tasks. [Dr. York & Satya: 11/21/05]
subclass of: task

data file URL
type: Class
comment: A string parameter that contains the URL of a data file.
subclass of: URL parameter

Bruker omniflex MALDI TOF mass spectrometer
type: Class
subclass of: MALDI-TOF mass spectrometer
subclass of: Restriction
  all values from: Bruker omniflex MALDI TOF ms raw data
  on property: generates raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]

Bruker omniflex MALDI TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

MS source ESI parameter collection
type: Class
comment: A collection of parameters controlling the operation of an electrospray ionization source of a mass spectrometer [Will & Satya 02/15/06]
equivalent class: Class
  intersection of: Restriction
    on property: has data part
    all values from: MS source ESI parameter
  intersection of: MS source parameter collection

SemURI instance ID
type: Class
subclass of: Restriction
  cardinality: 0
  on property: has SemURI concept ID
subclass of: SemURI parameter
comment: The second component of a semantic Universal Resource Identifier (semURI) module. This identifies a specific instance (within the context of a provenance chain) of a SemURI concept. It is important to note that the same SemURI_instance_ID can be used for two distinct instances of the same concept, as long as the two instances are not present at the same location of a single provenance chain. This allows the SemURI_instance_ID to be short and still insures that the SemURI as a whole is unique. Uniqueness stems from the entire SemURI, which consists of several SemURI modules. That is, two SemURIs can be unique even if they share a common SemURI module, just as two words can be unique even if they share a common letter of series of letters. [will & satya 03/03/06]
subclass of: Restriction
  all values from: string
  on property: has value

amino acid sequence
type: Class
subclass of: molecular sequence
comment: A parameter describing the sequence of amino acid residues of a peptide or protein. Amino acids are listed starting at the N-terminus and continuing to the C-terminus using standard one-letter amino acid nomenclature. The name of the amino acid sequence is same as the sequence string. [Dr. York & Satya: 06/10/05]

Finnigan LCQ classic ms raw data
type: Class
comment: The raw data output from this intrument. [James & Satya: 03/22/05]
subclass of: MS raw data native format

theoretical mass
type: Class
subclass of: mass
comment: A parameter describing the theoretical (calculated) mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05]

cyclotron analyzer
type: Class
comment: A type of MS analyzer
subclass of: MS analyzer

database search result Mascot peptide summary dataset
type: Class
subclass of: database search result Mascot HTML dataset
comment: The body of the Peptide Summary report contains a tabular listing of the proteins, sorted by descending protein score. [Dr. York & Satya: 07/19/05]

database search result Mascot HTML dataset
type: Class
comment: Following a Mascot db search, the data is saved in a HTML format. The results may further be converted into other representation formats. [James & Satya: 03/29/05]
subclass of: database search results Mascot data

inorganic solvent molecule
type: Class
comment: A solvent molecule that does not contain carbon, e.g., water.
subclass of: solvent molecule

solvent molecule
type: Class
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: substance accession number
comment: A molecule that exists as a liquid in the laboratory, and that can dissolve other molecules. E.G. water, methanol.
subclass of: Restriction
  all values from: Class
    complement of: isoelectric point
  on property: is described by
subclass of: small molecule
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: molecular sequence

physical task
type: Class
subclass of: task
comment: A task that is performed by a human or physical instrument working on a physical sample.

weak cation exchange HPLC column
type: Class
comment: A type of HPLC column
subclass of: HPLC column

SemURI concept ID
type: Class
subclass of: SemURI parameter
comment: The first component of a semantic Universal Resource Identifier (semURI) module. Each instance of this parameter maps the module to a specific concept in ProPreO. [will & satya 03/03/06]
subclass of: Restriction
  all values from: string
  on property: has value
subclass of: Restriction
  cardinality: 0
  on property: has SemURI concept ID

enzyme HPLC column
type: Class
comment: A type of HPLC column
subclass of: HPLC column

polypeptide
type: Class
subclass of: Restriction
  all values from: Class
    complement of: Class
      union of: DNA nucleotide sequence
      union of: RNA nucleotide sequence
  on property: is described by
comment: A biomolecule composed of amino acids connected by amide bonds. In ProPreO, a protein is distinguished from an oligopeptide mainly by its size (proteins are larger, and so are polypeptides rather than oligopeptides) . [Dr. York & Satya: 06/10/05]
subclass of: molecule
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: polynucleotide accession number
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: glycan accession number

DNA nucleotide sequence
type: Class
subclass of: molecular sequence
comment: A parameter describing the sequence of deoxynucleotides in a DNA molecule. Nucleotides are listed from the 5' end to the 3' end.

process time parameter
type: Class
comment: A parameter that describes the time within a process that an event occured. E.G., a "retention time" in HPLC or a "scan acquisition time" in mass spectrometry.
subclass of: process associated parameter

HPLC experimentally measured parameter
type: Class
subclass of: HPLC parameter
subclass of: experimentally measured parameter
comment: A parameter that is measured during an HPLC experiment - E.G. the detector signal intensity at a particular time.

HPLC time parameter
type: Class
subclass of: HPLC experimentally measured parameter
subclass of: HPLC instrumental operating parameter
comment: A parameter that describes the time (measured from the start of the experiment) within a HPLC experiment that an event occurs. This time parameter can be associated, for example, with a signal intensity or a buffer gradient condition.
subclass of: process time parameter

TOF analyzer
type: Class
comment: A type of MS analyzer
subclass of: MS analyzer

separate by size exclusion chromatography
type: Class
comment: The process of separating components by size-exclusion chromatography.
subclass of: separate by chromatography

separate by chromatography
type: Class
comment: The process of separating components by chromatography. [Dr. York & Satya: 11/21/05]
subclass of: separate components

HPLC microscale MALDI spotter
type: Class
subclass of: HPLC fraction collector
comment: An HPLC fraction collector that directs the eluant from an micro scale HPLC experiment onto specific locatons on a MALDI target for subsequent MALDI MS analysis.

Bruker ultraflex MALDI TOF mass spectrometer
type: Class
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker ultraflex MALDI TOF ms raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]
subclass of: MALDI-TOF mass spectrometer

Bruker ultraflex MALDI TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

quantify data
type: Class
comment: The computational processing in which a quantity (e.g. amount) is associated with various data elements.
subclass of: process data

separate by lectin affinity chromatography
type: Class
subclass of: separate by chromatography
comment: The process of separating components by lectin-affinity chromatography.

Micromass Q TOF ultima quadrupole time of flight ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

experimental chemical mass
type: Class
comment: A parameter describing the measured chemical mass of a particularmolecule or ion. [Dr. York & Satya: 06/13/05]
subclass of: experimental mass

experimental mass
type: Class
comment: A parameter describing the measured mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05]
subclass of: mass

HPLC data processing application
type: Class
subclass of: data processing application
comment: Application software used in processing/manipulating HPLC data. [James & Satya: 03/27/05]

data processing application
type: Class
subclass of: agent
comment: Application software used in processing/manipulating data. [James & Satya: 03/27/05]

mass spectrometer
type: Class
comment: A mass spectrometer separates and counts ions based on their mass to charge ratios. [James & Satya: 03/27/05]
subclass of: analytical instrument
subclass of: Restriction
  on property: has material part
  all values from: MS component
subclass of: Restriction
  all values from: MS raw data native format
  on property: generates raw data

fragment peptide N terminus index
type: Class
comment: A parameter describing the index (within the parent protein) of the N- terminus of a fragment peptide. [will & satya 04/25/06]
subclass of: molecular parameter

Agilent HPLC data processing application
type: Class
comment: The family of application software developed by Agilent for processing HPLC data. [James & Satya: 03/27/05]
subclass of: HPLC data processing application

power units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of power

fluorescence activated cell sorter
type: Class
comment: An instrument that performs a type of flow cytometry (cell counting), sorting cells in a suspension according to their fluorescence properties.
subclass of: analytical instrument

mz abundance pair
type: Class
subclass of: ms output data collection
equivalent class: Class
  intersection of: Restriction
    some values from: mass to charge ratio
    on property: has data part
  intersection of: Restriction
    some values from: ion abundance
    on property: has data part
comment: A typical mass spectral data pair consisting of a mass-to-charge (m/z) ratio and the abundance associated with that ratio

mass to charge ratio
type: Class
comment: A parameter describing the (measured or theoretical) mass-to-charge ratio (m/z) of a particular ion.
subclass of: ion parameter
subclass of: Restriction
  all values from: float
  on property: has value

material part of
type: TransitiveProperty
comment: This specialization of the 'part-of' relation is to relate material continuants (as defined in 'Relations in biomedical ontologies', Barry Smith et. al.). [Satya & Will 03/02/06]
type: ObjectProperty
sub property of: part of
range: material continuant
domain: material continuant

database search processing parameter collection
type: Class
comment: A collection of parameters required to perform a database search with ms, ms-ms data. [James & Satya: 03/27/05]
equivalent class: Class
  intersection of: operating parameter collection
  intersection of: database search data collection

database search data collection
type: Class
comment: A data collection that is used or generated by a database search with ms, ms-ms data
subclass of: process associated data collection

separate by dialysis
type: Class
comment: Separate components of a mixture by dialysis. The dialysis membrane allows some components to pass through while retaining other components.
subclass of: separate components

separate components
type: Class
subclass of: physical task
comment: The task of physcially spearating the components of a mixture.

nanoflow HPLC pump
type: Class
comment: A type of HPLC pump. [James & Satya: 01/31/05]
subclass of: HPLC pump

CARBANK ID
type: Class
subclass of: glycan accession number
comment: A parameter that specifies the identifier for a glycan record in the CARBANK database. URL: ftp://ncbi.nlm.nih.gov/repository/carbbank/ [Dr. York & Satya: 06/14/05]

Bruker microflex MALDI TOF ms raw data
type: Class
comment: The raw data output from this intrument. [James & Satya: 03/22/05]
subclass of: MS raw data native format

separate by HPLC
type: Class
comment: The process of separating components by high-performance liquid chromatography.
subclass of: separate by chromatography

MS analyzer mass range max
type: Class
subclass of: MS analyzer parameter
comment: A parameter that defines the maximum mass range associated with a MS experiment. Mass range is determined by the user and the instrument. It typically has a value from 0 to 500,000. [James & Satya: 02/24/05]
subclass of: Restriction
  on property: has units
  all values from: mass units

mass units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of mass

Bruker esquire6000 ion trap mass spectrometer
type: Class
subclass of: Restriction
  all values from: Bruker esquire6000 ion trap ms raw data
  on property: generates raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: ion trap mass spectrometer

Bruker esquire6000 ion trap ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

HPLC flowrate
type: Class
comment: A parameter that describes the eluant flow rate for an HPLC experiment. [James & Satya: 01/31/05]
subclass of: Restriction
  on property: has units
  all values from: flowrate units
subclass of: HPLC instrumental operating parameter

HPLC micro autosampler
type: Class
subclass of: HPLC autosampler
comment: A type of HPLC autosampler. [James & Satya: 01/31/05]

Bruker autoflex TOF TOF mass spectrometer
type: Class
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: tandem time of flight mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker autoflex TOF TOF ms raw data

mass percent
type: Class
comment: A parameter describing the amount of a particular substance in a mixture. The mass percent of the substance is its percent contribution to the total mass of the mixture. Sometimes mass percent is called weight/weight percent, and abbreviated %w/w.
subclass of: component amount

HPLC injection loop volume
type: Class
subclass of: HPLC instrumental operating parameter
subclass of: Restriction
  on property: has value
  all values from: float
comment: A parameter that describes the injuection loop volume for an HPLC experiment.
subclass of: Restriction
  on property: has units
  all values from: volume units

N-glycosylation consensus presence
type: Class
comment: A boolean parameter that describes whether a N-glycosylation consensus sequence is present in a peptide or protein. [will & satya 04/25/06]
subclass of: molecular parameter
subclass of: Restriction
  all values from: boolean
  on property: has value

HPLC detector signal
type: Class
subclass of: HPLC experimentally measured parameter
comment: A parameter that describes the detector signal measured at a particular time of an HPLC experiment.

Bruker microQTOF quadrupole time of flight mass spectrometer
type: Class
subclass of: quadrupole time of flight mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker microQTOF quadrupole time of flight ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

quadrupole time of flight mass spectrometer
type: Class
comment: A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]
subclass of: tandem mass spectrometer

source organ
type: Class
subclass of: Restriction
  on property: refers to material continuant
  all values from: organ
subclass of: biological source parameter
comment: A parameter that specifies the organ from which the biological sample is taken.

organ
type: Class
subclass of: biological continuant
comment: A specific biological organ, such as heart or leaf. Several OBO ontologies model anatomical features of organsims, including their organs, tissues, cells, etc. and additional semantic information can be specified by cross reference to these other ontologies.

micromass pkl ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. QTof users can export peak list data in either DTA or PKL format using the Micromass ProteinLynx package. The PKL format is similar to the DTA file format, but supports multiple MS/MS datasets in a single file. The first line of a PKL dataset contains the observed m/z, intensity, and charge state of the precursor peptide as a triplet of space separated values. Subsequent lines contain space separated pairs of fragment ion m/z and intensity values. Multiple MS/MS datasets are delimited by at least one blank line. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05]

processed gel electrophoresis data
type: Class
subclass of: gel electrophoresis experimental data collection
version info: TODO: Find out the various formats, softwares used...
comment: A data collection generated by a processing raw gel electrophoresis data. This data will include, for example 1. Spot location 2. Spot Intensity 3. Spot Identity [Dr. York & Satya: 06/28/05]

gel electrophoresis experimental data collection
type: Class
subclass of: experimentally measured data collection
subclass of: gel electrophoresis data collection
comment: A data collection generated by a gel electrophoresis experiment

MS analyzer interscan delay
type: Class
comment: A parameter that defines the time period between MS and MS-MS scans. [James & Satya: 02/24/05]
subclass of: MS analyzer parameter

database search result Mascot protein summary dataset
type: Class
comment: The body of the report contains a tabular summary of the best matching proteins. [Dr. York & Satya: 07/19/05]
subclass of: database search result Mascot HTML dataset

archaea
type: Class
comment: Organisms, including the Crenarchaeota, Euryarchaeota and Korarchaeota, with a cell structure that is similar to other prokaryotes, but with some biochemical features that are similar to eukaryotes, some similar to bacteria, and some unique to archaea.
subclass of: procaryotic organism

biochemical sample
type: Class
subclass of: molecular aggregate
comment: A molecular aggregate that has been prepared in the laboratory from a biological continuant.
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: Class
      union of: ion parameter
      union of: molecular parameter
subclass of: Restriction
  all values from: substance parameter
  on property: is described by

HPLC chromatogram text format data
type: Class
subclass of: HPLC chromatogram
comment: A data collection (chromatogram) generated by an HPLC experiment - This describes, two-column data which are signal vs time. The data columns are generally tab, space or comma separated. [James & Satya: 03/29/05]

manufacturer
type: Class
comment: The person or company that manufactures an instrument, reagent or other product.
subclass of: agent

Micromass Quatro micro triple quadrupole ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

GycO ID
type: Class
subclass of: glycan accession number
comment: A parameter that specifies the unique identifier for a glycan instance in glycan domain ontology: GlycO. URL: http://lsdis.cs.uga.edu/projects/glycomics/glyco/ [Dr. York & Satya: 06/13/05]

Bruker BioTOF Q quadrupole time of flight ms raw data
type: Class
comment: The raw data output from this intrument. [James & Satya: 03/22/05]
subclass of: MS raw data native format

MALDI matrix
type: Class
subclass of: Restriction
  all values from: small molecule
  on property: has material part
subclass of: molecular aggregate
comment: A molecular aggragate that is used in a MALDI source. The MALDI matrix absorbs energy from the laser, and this energy promotes transfer to the gas phase and ionizaton of the analyte.

Micromass Q TOF micro quadrupole time of flight mass spectrometer
type: Class
subclass of: Restriction
  all values from: Micromass Q TOF micro quadrupole time of flight ms raw data
  on property: generates raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: Restriction
  all values from: Class
    union of: micromass pkl ms-ms peak list
    union of: Finnigan Sequest DTA ms-ms peak list
  on property: generates ms-ms peak list
subclass of: quadrupole time of flight mass spectrometer

Finnigan Sequest DTA ms-ms peak list
type: Class
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. The DTA format is very simple. The first line contains the singly protonated peptide mass (MH+) and the peptide charge state as a pair of space separated values. Subsequent lines contain space separated pairs of fragment ion m/z and intensity values. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05]
subclass of: ms-ms peak list

generates ms-ms peak list
type: ObjectProperty
sub property of: generates processed data
domain: tandem mass spectrometer
range: ms-ms peak list
comment: Peak list produced from tandem ms experiments. [James & Satya: 03/27/05]

time units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of time

gel electrophoresis data collection
type: Class
subclass of: process associated data collection
comment: A data collection used or generated by gel electrophoresis experiments

UNIPROT accession number
type: Class
comment: A parameter that specifies the unique identifier for a particular protein in the UNIPROT (formerly SWISSPROT) database. URL: www.uniprot.org/ [Dr. York & Satya: 06/14/05]
subclass of: protein accession number

MALDI source
type: Class
comment: Defines the type of source. [James & Satya: 02/24/05]
subclass of: MS source

SemURI module
type: Class
subclass of: annotation associated data collection
equivalent class: Class
  intersection of: Restriction
    some values from: SemURI concept ID
    on property: has data part
  intersection of: Restriction
    some values from: SemURI instance ID
    on property: has data part
  intersection of: Restriction
    on property: has data part
    cardinality: 2
comment: This describes the two-component, basic building block of the Semantic URI provenance scheme. The two components are: 1- SemURI_concept_ID 2- SemURI_instance_ID [will & satya 03/03/06]

classify data
type: Class
subclass of: process data
comment: The computational processing in which data elements are matched to a spcific group to which they belong. This includes: a) identifying molecules associated with experimental data features such as ion masses (e.g., MASCOT analysis) b) categorize features in data using a set of parameters. For example, distinguish peptides from glycopeptides [Dr. York & Satya: 11/21/05]

HPLC standard well plate autosampler
type: Class
comment: A type of HPLC autosampler.
subclass of: HPLC autosampler

Bruker autoflex MALDI TOF mass spectrometer
type: Class
subclass of: Restriction
  all values from: Bruker autoflex MALDI TOF ms raw data
  on property: generates raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]
subclass of: MALDI-TOF mass spectrometer

meta data file URL
type: Class
subclass of: URL parameter
comment: A string parameter that contains the URL of a meta-data file.

Proteinlynx micromass ms-ms survey data processing parameters collection
type: Class
subclass of: MS data processing parameter collection
comment: The collection of processing parameters used by Proteinlynx when converting a ms/ms survey '.raw' file into a '.pkl' or a '.dta' file, when using Proteinlynx. [James & Satya: 04/01/05]

quantify components
type: Class
comment: The complex task of quantifying the components of a mixture. This may involve, for example, HPLC of the mixture (i.e. separate_by_HPLC) followed by computational peak picking and signal integration (i.e., quantify_data).
subclass of: hybrid task

organic solvent molecule
type: Class
subclass of: small organic molecule
subclass of: solvent molecule
comment: A solvent molecule that contains carbon, e.g., methanol.

denovo sequencing processing parameter collection
type: Class
comment: A collection of parameters required to perform a denovo sequencing with ms-ms data. [James & Satya: 03/27/05]
equivalent class: Class
  intersection of: operating parameter collection
  intersection of: denovo sequencing data collection

Micromass MALDI micro MX MALDI TOF mass spectrometer
type: Class
subclass of: Restriction
  all values from: Micromass MALDI micro MX MALDI TOF ms raw data
  on property: generates raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]
subclass of: MALDI-TOF mass spectrometer

Agilent mass spectrometer data processing application
type: Class
subclass of: MS data processing application
comment: Application software developed by Agilent for processing mass spectrometer data. [James & Satya: 03/27/05]

Bruker BioTOF Q quadrupole time of flight mass spectrometer
type: Class
subclass of: quadrupole time of flight mass spectrometer
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: Restriction
  all values from: Bruker BioTOF Q quadrupole time of flight ms raw data
  on property: generates raw data

HPLC vacuum degasser
type: Class
comment: An HPLC instrument component that uses a vacuum to remove dissolved gas from a sample or eluant before it is pumped through the HPLC column.
subclass of: HPLC component

Finnigan LTQ linear ion trap ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

absolute mass
type: Class
comment: A parameter describing the total mass of a particular substance (e.g., 5 grams of NaCl) in a molecular aggregate
subclass of: absolute amount

HPLC analytical scale fraction collector
type: Class
comment: An HPLC fraction collector that directs the eluant from an analytical scale HPLC experiment. [James & Satya: 01/31/05]
subclass of: HPLC fraction collector

MS source MALDI parameter collection
type: Class
equivalent class: Class
  intersection of: MS source parameter collection
  intersection of: Restriction
    all values from: MS source MALDI parameter
    on property: has data part
comment: A collection of parameters controlling the operation of a matrix-assisted laser-desorption ionization source of a mass spectrometer [Will & Satya 02/15/06]

experimental monoisotopic mass
type: Class
comment: A parameter describing the measured monoisotopic mass of a particularmolecule or ion. [Dr. York & Satya: 06/13/05]
subclass of: experimental mass

Finnigan LTQ FT mass spectrometer
type: Class
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: Restriction
  all values from: Class
    union of: Finnigan ASC ms-ms peak list
    union of: Finnigan Sequest DTA ms-ms peak list
  on property: generates ms-ms peak list
subclass of: Restriction
  on property: generates raw data
  all values from: Finnigan LTQ FT ms raw data
subclass of: hybrid tandem mass spectrometer

fragment peptide C terminus index
type: Class
subclass of: molecular parameter
comment: A parameter describing the index (within the parent protein) of the C- terminus of a fragment peptide. [will & satya 04/25/06]

HPLC chromatogram XML format data
type: Class
comment: A data collection (chromatogram) generated by an HPLC experiment - This describes, two-column data which are signal vs time. The data columns are in XML. [James & Satya: 03/29/05]
subclass of: HPLC chromatogram

theoretical monoisotopic mass
type: Class
subclass of: theoretical mass
comment: A parameter describing the theoretical (calculated) monoisotopic mass of a particular molecule or ion. [Dr. York & Satya: 06/13/05]

Finnigan LTQ linear ion trap mass spectrometer
type: Class
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: ion trap mass spectrometer
subclass of: Restriction
  all values from: Finnigan LTQ linear ion trap ms raw data
  on property: generates raw data
subclass of: Restriction
  on property: generates ms-ms peak list
  all values from: Class
    union of: Finnigan ASC ms-ms peak list
    union of: Finnigan Sequest DTA ms-ms peak list

CCSD ID
type: Class
subclass of: glycan accession number
comment: A parameter that specifies the unique identifier for a glycan structure in the CARBANK database. URL: http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm#ccsd [Dr. York & Satya: 06/14/05]

HPLC detection wavelength
type: Class
comment: A parameter that describes the detection wavelength of the HPLC detector, which may be either an absorbance detector or a fluorescence detector. [James & Satya: 01/31/05]
subclass of: Restriction
  on property: has units
  all values from: length units
subclass of: HPLC instrumental operating parameter
subclass of: Restriction
  all values from: float
  on property: has value

MS analyzer mass range min
type: Class
comment: A parameter that defines the minimum mass range associated with a MS experiment.
subclass of: MS analyzer parameter
subclass of: Restriction
  all values from: mass units
  on property: has units

Finnigan LCQ classic mass spectrometer
type: Class
subclass of: Restriction
  on property: generates ms-ms peak list
  all values from: Class
    union of: Finnigan ASC ms-ms peak list
    union of: Finnigan Sequest DTA ms-ms peak list
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: ion trap mass spectrometer
subclass of: Restriction
  all values from: Finnigan LCQ classic ms raw data
  on property: generates raw data

HPLC manual injector
type: Class
subclass of: HPLC component
comment: An HPLC component that is used for manual injection of the sample onto the column. [James & Satya: 01/31/05]

theoretical mass to charge ratio
type: Class
subclass of: mass to charge ratio
comment: A parameter describing the theoretical mass-to-charge ratio (m/z) of a particular ion. [will & satya 03/02/06]

PerSeptive PKS 51 ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. PSD peak lists exported from Grams as .PKS files contain data from a single PSD spectrum. Since the .PKS format does not include details of the precursor peptide m/z, this information must be entered manually into the PRECURSOR and CHARGE form fields. This limitation also means that multiple spectra cannot be merged into a single data file. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05]

MS source MALDI matrix
type: Class
equivalent class: Class
  intersection of: substance identifier
  intersection of: MS source MALDI parameter
comment: A parameter that defines the matrix used in the MALDI analysis. It may be of multiple types like: a) DHB b) Alpha-Cyano [James & Satya: 02/24/05]
subclass of: Restriction
  all values from: MALDI matrix
  on property: refers to material continuant

gel electrophoresis processing parameter collection
type: Class
comment: A collection of parameters required to perform a gel electrophoresis experiment. [James & Satya: 03/27/05]
equivalent class: Class
  intersection of: operating parameter collection
  intersection of: gel electrophoresis data collection

size exclusion HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

separate by filtration
type: Class
comment: Separate components of a mixture by filtration. The filter allows some components to pass through while retaining other components.
subclass of: separate components

experimental mass to charge ratio
type: Class
comment: A parameter describing the measured mass to charge ratio (m/z) of a particular ion.
subclass of: mass to charge ratio
subclass of: MS experimentally measured parameter

Bruker microflex MALDI TOF mass spectrometer
type: Class
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]
subclass of: MALDI-TOF mass spectrometer
subclass of: Restriction
  all values from: Bruker microflex MALDI TOF ms raw data
  on property: generates raw data

isocratic HPLC pump
type: Class
comment: A type of HPLC pump. [James & Satya: 01/31/05]
subclass of: HPLC pump

electric sector analyzer
type: Class
subclass of: MS analyzer
comment: A type of MS analyzer

UV spectrometer
type: Class
subclass of: analytical instrument
comment: An instrument that measures the transmittance of ultraviolet light through a sample (usually a liquid).

HPLC standard autosampler
type: Class
subclass of: HPLC autosampler
comment: A type of HPLC autosampler. [James & Satya: 01/31/05]

theoretical chemical mass
type: Class
subclass of: theoretical mass
comment: A parameter describing the theoretical (calculated) chemical mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05]

Micromass Quatro micro triple quadrupole mass spectrometer
type: Class
subclass of: Restriction
  all values from: Micromass Quatro micro triple quadrupole ms raw data
  on property: generates raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: triple quadrupole mass spectrometer

Bruker Daltomics mass spectrometer data processing application
type: Class
comment: Application software developed by Bruker Daltonics for processing mass spectrometer data. [James & Satya: 03/27/05]
subclass of: MS data processing application

KEGG ID
type: Class
comment: A parameter that specifies the unique glycan identifier in the KEGG database. URL: http://www.genome.jp/kegg/ [Dr. York & Satya: 06/14/05]
subclass of: glycan accession number

weak anion exchange HPLC column
type: Class
comment: A type of HPLC column
subclass of: HPLC column

Micromass QTOF 2 quadrupole time of flight mass spectrometer
type: Class
subclass of: Restriction
  on property: generates ms-ms peak list
  all values from: Class
    union of: Finnigan Sequest DTA ms-ms peak list
    union of: micromass pkl ms-ms peak list
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]
subclass of: Restriction
  on property: generates raw data
  all values from: Micromass QTOF 2 quadrupole time of flight ms raw data
subclass of: quadrupole time of flight mass spectrometer

database search results Sequest data
type: Class
subclass of: database search output data collection
comment: A data collection that is generated by a Sequest database search with ms, ms-ms data [James & Satya: 03/29/05]

MS time parameter
type: Class
subclass of: process time parameter
subclass of: MS parameter
comment: A parameter that describes the time within a mass spectrometry that an event occurs. E.G., the time (measured from the start of the experiment) that a particular mass spectrum was recorded.

MS analyzer mode
type: Class
comment: A parameter that defines the analyzer mode associated with a MS experiment. This parameter can have values of positive or negative. It describes the charge of the ions that are detected. [James & Satya: 02/24/05]
subclass of: MS analyzer parameter

normal-phase HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

MS analyzer TOF type
type: Class
subclass of: Restriction
  all values from: TOF analyzer
  on property: refers to material continuant
subclass of: Restriction
  on property: has units
  cardinality: 0
subclass of: MS analyzer parameter
comment: A parameter that defines the type of TOF analyzer. It may either be: a) Reflectron or b) Linear [James & Satya: 02/24/05]

strong anion exchange HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

eucaryotic organism
type: Class
subclass of: organism
comment: An organism whose cells contain a nucleus and internal membranes. [Dr. York & Satya: 06/28/05]

salt
type: Class
subclass of: Restriction
  all values from: Class
    complement of: substance accession number
  on property: is described by
subclass of: Restriction
  all values from: Class
    complement of: molecular sequence
  on property: is described by
subclass of: Restriction
  on property: has material part
  all values from: ion
subclass of: molecule
comment: A chemical compound composed of at least one cation (positive ion) and at least one anion (negative ion).
subclass of: Restriction
  all values from: Class
    complement of: isoelectric point
  on property: is described by

chemical abstracts accession number
type: Class
subclass of: substance accession number
comment: A parameter that corresponds to the Chemical Abstrracts Accession number of a molecule.
subclass of: Restriction
  on property: has units
  cardinality: 0

Micromass Q TOF ultima quadrupole time of flight mass spectrometer
type: Class
subclass of: quadrupole time of flight mass spectrometer
subclass of: Restriction
  all values from: Class
    union of: Finnigan Sequest DTA ms-ms peak list
    union of: micromass pkl ms-ms peak list
  on property: generates ms-ms peak list
subclass of: Restriction
  on property: generates raw data
  all values from: Micromass Q TOF ultima quadrupole time of flight ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

raw gel image electrophoresis data
type: Class
subclass of: gel electrophoresis experimental data collection
comment: A data collection generated by a gel electrophoresis experiment - this corresponds to an image of the gel, stored in a file format. [James & Satya: 03/29/05]

MS analyzer parameter collection
type: Class
subclass of: Restriction
  on property: has data part
  all values from: MS analyzer parameter
comment: A collection of parameters controlling the operation of the analyzer of a mass spectrometer [James & Satya: 02/24/05]
subclass of: MS instrument setup parameter collection

Spectrum mill application
type: Class
subclass of: Agilent mass spectrometer data processing application
comment: Application software developed by Agilent for processing mass spectrometer data. [James & Satya: 03/27/05]

volume percent
type: Class
subclass of: component amount
comment: A parameter describing the amount of a particular substance in a mixture. The volume percent of the substance is its percent contribution to the total volume of the mixture. Sometimes volume percent is called volume/volume percent, and abbreviated %v/v.

MS analyzer focus mass
type: Class
comment: A parameter that defines the center of the mass range or the center of the calibration curve for the given mass range. [James & Satya: 02/24/05]
subclass of: Restriction
  all values from: float
  on property: has value
subclass of: Restriction
  all values from: mass units
  on property: has units
subclass of: MS analyzer parameter

GPS Explorer application
type: Class
comment: Application software developed by Applied Bio Systems for processing mass spectrometer data. [James & Satya: 03/27/05]
subclass of: Applied Bio Systems mass spectrometer data processing application

task part of
type: ObjectProperty
domain: task
sub property of: part of
type: TransitiveProperty
comment: This specialization of the 'part-of' relation is to relate immaterial continuants (as defined in 'Relations in biomedical ontologies', Barry Smith et. al.). [Satya & Will 03/02/06]
range: task

part of
type: TransitiveProperty
comment: One of the top level relations, as defined in the 'Relations in biomedical ontologies', Barry Smith et. al. Genome Biology 2005, 6:R46. Thsi relation has been defined for all the top level classes in ProPreO (through subsumption from owl:Thing) i.e. all classes in ProPreO have a or are a 'part-of' another ProPreO class. [Satya & Will 03/01/2006]
inverse of: has part
type: ObjectProperty

has provenance property
type: ObjectProperty
comment: An abstract object property subsuming object properties that map to an objectified and classified parameter. The objectified parameter wraps a datum value associated with it. For example, has_mass maps to objects of the class "mass", which have the data property "has_value". Then, "has_value" is restricted to float values (amu) for the class "mass"

is effect of
type: ObjectProperty
comment: This is an 'abstract' property that subsumes properties that denote causality in the passive voice. [Will & Satya: 01/19/06]

has biological source
type: ObjectProperty
range: biological continuant
comment: Associates a biomolecule with its biological source. [Dr. York & Satya: 06/28/05]
domain: Class
  union of: molecule
  union of: biochemical sample

data part of
type: ObjectProperty
range: data
comment: This specialization of the 'part-of' relation is to relate immaterial continuants (as defined in 'Relations in biomedical ontologies', Barry Smith et. al.). [Satya & Will 03/02/06]
domain: data
sub property of: part of
type: TransitiveProperty

is cause of
type: ObjectProperty
comment: This is an 'abstract' property that subsumes properties that denote causality in the active voice. [Will & Satya: 01/19/06]

has agent
type: ObjectProperty
comment: This object property is subsumed by "has_agent" object property as defined in Barry Smith et. al. "Relations in biomedical ontologies", Genome Biology, Vol 6, Article R46.
range: agent
domain: task

has part
type: ObjectProperty
comment: This object property describes the canonical composition of all data collection - they are made up of either parameters or data collection itself. [Satya - 02/23/06]
type: TransitiveProperty
inverse of: part of

generates ms peak list
type: ObjectProperty
comment: All mass spectrometers can produce peak lists containing masses and intensities. Different types of mass spectrometers can produce different formats of ms peak lists. [James & Satya: 03/27/05]
domain: mass spectrometer
sub property of: generates processed data

has parent protein
type: ObjectProperty
domain: peptide
range: polypeptide
comment: Defines the protein from which the peptide was cleaved. The peptide is a specific entity and not a generic sequence. [Dr. York & Satya: 06/10/05]

linear TOF MS analyzer
type: MS analyzer TOF type
has value: linear TOF analyzer

liters
type: volume units
has value: liters
comment: the physical units of volume in liters

micrometers
type: length units
has value: micrometers
comment: the physical units of length in micrometers, or 0.000001 meters

volts
type: electrical potential units
comment: The units of electrical potential defined as volts, which can also be expressed as Joules per coulomb
has value: volts

microliters per minute
type: flowrate units
comment: the physical units of flowrate in microliters per minute
has value: microliters per minute

minutes
type: time units
has value: minutes
comment: the physical units of time in minutes

mg
type: mass units
comment: the physical units of mass in milligrams
has value: milligrams

alpha-cyano-4-hydroxycinnamic acid
type: MS source MALDI matrix
comment: A MALDI matrix composed of alpha-cyano-4-hydroxycinnamic acid
has value: alpha-cyano-4-hydroxycinnamic acid
refers to material continuant: alpha-cyano-4-hydroxycinnamic acid MALDI matrix

alpha-cyano-4-hydroxycinnamic acid MALDI matrix
type: MALDI matrix
has material part: alpha-cyano-4-hydroxycinnamic acid
comment: Defines a matrix composed of alpha-Cyano-4-hydxoxycinnamic_acid, used for MALDI MS

alpha-cyano-4-hydroxycinnamic acid
type: small organic molecule
is described by: CAS 28166-41-8
comment: An aromatic molecule (alpha-cyano-4-hydroxycinnamic acid) used as a MALDI matrix

CAS 28166-41-8
type: chemical abstracts accession number
comment: The CAS number of alpha-cyano-4-hydroxycinnamic acid
has value: 28166-41-8
refers to material continuant: alpha-cyano-4-hydroxycinnamic acid

millivolts
type: electrical potential units
comment: The units of electrical potential defined as millivolts, or thousandths of a volt.
has value: millivolts

Homo sapiens
type: source organism
has value: Homo sapiens
refers to material continuant: Homo sapiens
label: Man

Homo sapiens
type: eucaryotic organism
label: Man
comment: Man [Dr. York & Satya: 06/28/05]

molarity units
type: concentration units
has value: moles per liter
comment: the physical units of concentration in moles per liter

nanometers
type: length units
comment: the physical units of length in nanometers, or 0.000000001 meters
has value: nanometers

N-glycosylation consensus presence true
type: N-glycosylation consensus presence
has value: true

micrograms
type: mass units
has value: micrograms
comment: the physical units of mass in micrograms

N-glycosylation consensus presence false
type: N-glycosylation consensus presence
has value: false

ng
type: mass units
has value: nanograms
comment: the physical units of mass in nanograms

DHB
type: MS source MALDI matrix
comment: A MALDI matrix composed of dihydroxybenzoic acid
has value: DHB
refers to material continuant: DHB MALDI matrix

DHB MALDI matrix
type: MALDI matrix
comment: Defines a matrix composed of 2,5-dihydroxybenzoic acid, used for MALDI MS
has material part: 2-5-dihydroxybenzoic acid

2-5-dihydroxybenzoic acid
type: small organic molecule
comment: An aromatic molecule (2-5-dihydroxybenzoic_acid) used as a MALDI matrix
is described by: CAS 490-79-9

CAS 490-79-9
type: chemical abstracts accession number
refers to material continuant: 2-5-dihydroxybenzoic acid
has value: 490-79-9
comment: The CAS number of 2,5-dihydroxybenzoic acid

milliliters
type: volume units
comment: the physical units of volume in milliliters
has value: milliliters

negative MS mode
type: MS analyzer mode
has value: negative mode

reflectron TOF MS analyzer
type: MS analyzer TOF type
has value: reflectron TOF analyzer

millimeters
type: length units
has value: millimeters
comment: the physical units of length in millimeters, or 0.001 meters

amu
type: mass units
has value: amu
comment: 1 amu ≈ 1.66053886 × 10E-27 kg

hours
type: time units
has value: hours
comment: the physical units of time in hours

C
type: electrical charge units
has value: coulombs
comment: The units of electrical charge defined as coulombs, which can also be expresses as Amperes seconds. One coulomb is equivalent to the charge of 6.24151E18 electrons.

deleted
comment: The ChEBI ID of alpha-cyano-4-hydroxycinnamic acid

water solvent
type: solvent
comment: A collection of water molecules, acting as a solvent
has material part: water

water
type: inorganic solvent molecule
is described by: CHEBI_15377
comment: A molecule of water, the most common solvent for HPLC
is described by: CAS 7732-18-5

CHEBI_15377
type: CHEBI ID
has value: CHEBI:15377
comment: The ChEBI ID for water
refers to material continuant: water

CAS 7732-18-5
type: chemical abstracts accession number
comment: The CAS number of water
has value: 7732-18-5
refers to material continuant: water

nanoliters per minute
type: flowrate units
has value: nanoliters per minute
comment: the physical units of flowrate in nanoliters per minute

milliliters per minute
type: flowrate units
comment: the physical units of flowrate in milliliters per minute
has value: milliliters per minute

e
type: electrical charge units
comment: The elementary electrical charge is the charge of a single electron
has value: e
label: q

milliseconds
type: time units
comment: the physical units of time in milliseconds
has value: milliseconds

microliters
type: volume units
has value: microliters
comment: the physical units of volume in microliters

kg
type: mass units
has value: kilograms
comment: the physical units of mass in kilograms

seconds
type: time units
comment: the physical units of time in seconds
has value: seconds

g
type: mass units
comment: the physical units of mass in grams
has value: grams