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]
associates the peptide with the enzyme that released it. [Dr. York & Satya: 06/28/05]
Peak list produced from tandem ms experiments. [James & Satya: 03/27/05]
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]
This property enables mapping of each concept in ProPreO to a concept in the SemURI framework. [will & satya 03/03/06]
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.
Associates a biomolecule with its biological source. [Dr. York & Satya: 06/28/05]
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.
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]
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]
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"
This is an 'abstract' property that subsumes properties that denote causality in the active voice. [Will & Satya: 01/19/06]
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]
This is an 'abstract' property that subsumes properties that denote causality in the passive voice. [Will & Satya: 01/19/06]
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]
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]
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]
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]
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]
The raw data output from this instrument. [James & Satya: 03/22/05]
A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]
A High Performance Liquid Chromatograph manufactured by Agilent Technologies. [James & Satya: 01/31/05]
The family of application software developed by Agilent for processing HPLC data. [James & Satya: 03/27/05]
Application software developed by Agilent for processing mass spectrometer data. [James & Satya: 03/27/05]
Application software developed by Applied Bio Systems for processing mass spectrometer data. [James & Satya: 03/27/05]
A type of tandem mass spectrometer. [James & Satya: 03/27/05]
The raw data output from this instrument. [James & Satya: 03/27/05]
The raw data output from this intrument. [James & Satya: 03/27/05]
The raw data output from this intrument. [James & Satya: 03/22/05]
Application software developed by Bruker Daltonics for processing mass spectrometer data. [James & Satya: 03/27/05]
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]
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]
A parameter that corresponds to the CHEBI ID from the ChEBI Ontology http://www.ebi.ac.uk/chebi/
A parameter describing the sequence of deoxynucleotides in a DNA molecule. Nucleotides are listed from the 5' end to the 3' end.
For for > microlitre/min flow rates. [James & Satya: 02/24/05]
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]
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]
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]
An HPLC fraction collector that directs the eluant from an analytical scale HPLC experiment. [James & Satya: 01/31/05]
An HPLC component that is programmed to automatically inject samples into the HPLC column. [James & Satya: 01/31/05]
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]
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]
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]
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]
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.
A component of a hgh-performance liquid chromatograph
A data collection used or generated by a high performance liquid chromatography experiment
Application software used in processing/manipulating HPLC data. [James & Satya: 03/27/05]
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]
An HPLC instrument component that detects molecules that are eluted from the HPLC column. [James & Satya: 01/31/05]
A parameter that describes the detector signal measured at a particular time of an HPLC experiment.
A type of HPLC detector. [James & Satya: 01/31/05]
A parameter that describes the excitation wavelength of a fluorescence HPLC detector. [James & Satya: 01/31/05]
A parameter that is measured during an HPLC experiment - E.G. the detector signal intensity at a particular time.
A parameter that describes the eluant flow rate for an HPLC experiment. [James & Satya: 01/31/05]
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.
A collection of parameters that describe the solvent gradient for an HPLC run [Dr. York & Satya: 05/17/05]
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]
A parameter that describes the injuection loop volume for an HPLC experiment.
A parameter that defines the operating state of the chromatograph during data collection
An HPLC component that is used for manual injection of the sample onto the column. [James & Satya: 01/31/05]
A type of HPLC autosampler. [James & Satya: 01/31/05]
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.
An HPLC fraction collector that directs the eluant from an microscale HPLC experiment. [James & Satya: 01/31/05]
A collection of parameters required to perform or analyze an HPLC run. [Dr. York & Satya: 05/17/05]
A parameter that is used/created/generated during the acquisition or processing of HPLC data
An HPLC component that pumps the eluant through the HPLC column, usually at high pressure and at a tightly controlled flow rate.
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.
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.
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.
A parameter that specifies the unique glycan identifier in the KEGG database. URL: http://www.genome.jp/kegg/ [Dr. York & Satya: 06/14/05]
A parameter that specifies the unique glycan identifier in SWEETDB. URL: http://www.glycosciences.de/sweetdb/index.php [Dr. York & Satya: 06/13/05]
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]
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.
Defines the type of source. [James & Satya: 02/24/05]
A mass spectromete component that separates ions according to their mass to charge ratio. Ions are produced in the ion source.
A parameter that defines the type of TOF analyzer. It may either be: a) Reflectron or b) Linear [James & Satya: 02/24/05]
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]
A parameter that defines the time period between MS and MS-MS scans. [James & Satya: 02/24/05]
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]
A parameter that defines the minimum mass range associated with a MS experiment.
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]
A parameter that defines the operating state of the mass spectrometer analyzer during data collection [Will & Satya 02/15/06]
A collection of parameters controlling the operation of the analyzer of a mass spectrometer [James & Satya: 02/24/05]
A parameter that defines the length of time for an MS or MS-MS scan. [James & Satya: 02/24/05]
A data collection used or generated by a mass spectrometry experiment
Application software used in processing/manipulating ms or ms-ms data. [James & Satya: 03/27/05]
A parameter that is used by an application that processes mass spectral data
A collection of computational parameters required to process ms or ms-ms data [James & Satya: 03/27/05]
This is for self-manufactured or modified that are not found under the mass spectrometer instruments. [James & Satya: 02/24/05]
A parameter that is measured during an MS experiment - E.G. the abundance of an ion having a particular m/z value.
A collection of instrumental parameters required to record mass spectral data [James & Satya: 03/27/05]
A parameter that defines the operating state of the mass spectrometer during data collection
A collection of parameters required to perform a task that generates or processes mass spectral data
A parameter that is used/created/generated during the acquisition or processing of MS data [Will & Satya: 01/19/06]
A collection of mass spectral data that has NOT been computationally processed, except that its digital format has been modified
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]
A parameter that defines the voltage applied to the ESI capillary. [James & Satya: 02/24/05]
A parameter associated with an electrospray ionization source.
A collection of parameters controlling the operation of an electrospray ionization source of a mass spectrometer [Will & Satya 02/15/06]
A parameter that defines the intensity of the laser used in the MS experiment. [James & Satya: 02/24/05]
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]
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]
A parameter associated with a matrix assisted laser induced ionization source. [James & Satya: 02/24/05]
A collection of parameters controlling the operation of a matrix-assisted laser-desorption ionization source of a mass spectrometer [Will & Satya 02/15/06]
A parameter that defines the voltage applied to the inlet cone. [James & Satya: 02/24/05]
A parameter that defines the operating state of the mass spectrometer ion source during data collection [Will & Satya 02/15/06]
A collection of parameters controlling the operation of the ion source of a mass spectrometer [James & Satya: 02/24/05]
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.
Application software developed by Micromass for processing mass spectrometer data. [James & Satya: 03/27/05]
A data collection produced by performing Proteinlynx denovo sequecing. [James & Satya: 03/29/05]
A boolean parameter that describes whether a N-glycosylation consensus sequence is present in a peptide or protein. [will & satya 04/25/06]
Electrospray source for flow rates < 3 microlitres/min. [James & Satya: 02/24/05]
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]
A data collection produced by performing PEAKKS denovo sequecing. [James & Satya: 03/29/05]
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]
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]
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]
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]
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]
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]
A parameter describing the sequence of nucleotides in an RNA molecule. Nucleotides are listed from the 5' end to the 3' end.
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]
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.
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]
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]
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]
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.
Application software developed by ThermoElectron for processing mass spectrometer data. [James & Satya: 03/27/05]
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]
A string parameter that specifies the location of a resource (such as a data file) on the internet - I.e., a Universal Resource Locator
An instrument that measures the transmittance of ultraviolet light through a sample (usually a liquid).
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]
A parameter describing the total mass of a particular substance (e.g., 5 grams of NaCl) in a molecular aggregate
A parameter describing the total volume of a particular substance (e.g., 5 Liters of water) in a molecular aggregate
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
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]
An analytical instrument is a piece of hardware designed to measure a parameter or analyze a sample.
a data collection that is used to annotate other data
A parameter used in the annotation of data
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.
A diverse group of prokaryotic organisms, distinct from the Archaea.
A type of HPLC pump. [James & Satya: 01/31/05]
A molecular aggregate that has been prepared in the laboratory from a biological continuant.
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.
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.
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
A parameter that corresponds to the Chemical Abstrracts Accession number of a molecule.
A chemical agent is a chemical or molecule (such as an enzyme) that implements or initiates a molecular process.
A material continuant that is described chiefly with respect to its chemical composition.
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]
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.
A task involved in the processing of data by a computational application. [Dr. York & Satya: 11/21/05]
A parameter defining the physical units of concentration
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]
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]
A string parameter that contains the URL of a data file.
Application software used in processing/manipulating data. [James & Satya: 03/27/05]
A parameter that is used by a data processing application
A data collection that is used or generated by a database search with ms, ms-ms data
A data collection that is generated by a database search with ms, ms-ms data [James & Satya: 03/27/05]
A collection of parameters required to perform a database search with ms, ms-ms data. [James & Satya: 03/27/05]
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]
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]
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]
The body of the report contains a tabular summary of the best matching proteins. [Dr. York & Satya: 07/19/05]
A data collection that is generated by a Matrix Science Mascot database search with ms, ms-ms data
A data collection that is generated by a Sequest database search with ms, ms-ms data [James & Satya: 03/29/05]
A data collection that is generated by a Spectrum Mill database search with ms, ms-ms data [James & Satya: 03/29/05]
A data collection used or generated by a denovo sequencing process with ms-ms data.
A data collection generated by a denovo sequencing process with ms-ms data. [James & Satya: 03/27/05]
A collection of parameters required to perform a denovo sequencing with ms-ms data. [James & Satya: 03/27/05]
A parameter describing the units of electrical potential
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]
An enzyme is a protein or protein complex that catalyzes a specific set of chemical reactions.
An organism whose cells contain a nucleus and internal membranes. [Dr. York & Satya: 06/28/05]
A parameter describing the measured chemical mass of a particularmolecule or ion. [Dr. York & Satya: 06/13/05]
A parameter describing the measured abundance of a particular ion.
A parameter describing the measured charge of a particular ion.
Measured from an experiment. [Dr. York & Satya: 06/28/05]
A parameter describing the measured mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05]
A parameter describing the measured mass to charge ratio (m/z) of a particular ion.
A parameter describing the measured monoisotopic mass of a particularmolecule or ion. [Dr. York & Satya: 06/13/05]
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.
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.
A fluorescence spectrometer measures the intensity of light that is re-emitted by a fluorescent molecule.
An instrument that performs a type of flow cytometry (cell counting), sorting cells in a suspension according to their fluorescence properties.
The type of tandem_mass_spectrometer. [James & Satya: 03/27/05]
A parameter describing the index (within the parent protein) of the C- terminus of a fragment peptide. [will & satya 04/25/06]
A parameter describing the index (within the parent protein) of the N- terminus of a fragment peptide. [will & satya 04/25/06]
A data collection used or generated by gel electrophoresis experiments
A data collection generated by a gel electrophoresis experiment
A collection of parameters required to perform a gel electrophoresis experiment. [James & Satya: 03/27/05]
A biomolecule composed of glycosyl residues. A glycan is a type of carbohydrate molecule. [Dr. York & Satya: 06/10/05]
A parameter that specifies the unique identifierfor a glycan. [Dr. York & Satya: 06/13/05]
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).
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.
A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]
A task that combines both physical and computational tasks. [Dr. York & Satya: 11/21/05]
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).
A solvent molecule that does not contain carbon, e.g., water.
A part of a scientific instrument. Many instruments are modular, assembled by combining several interacting components.
An electrically charged chemical species, which may be a single atom (e.g., Na+), or many atoms (e.g., NH4+).
A parameter describing the (measured or theoretical) abundance of a particular ion.
A parameter describing the (measured or theoretical) charge of a particular ion.
A parameter describing the properties of an ion.
Describes the pH at which a zwitter ionic molecule has no charge also called pI. [Dr. York & Satya: 06/28/05]
A parameter that defines the units used to describe the intensity of a laser pulse
A parameter defining the physical units of length
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
The person or company that manufactures an instrument, reagent or other product.
Describes the molecular mass of a molecule or ion . [Dr. York & Satya: 06/13/05]
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.
A mass spectrometer separates and counts ions based on their mass to charge ratios. [James & Satya: 03/27/05]
A parameter describing the (measured or theoretical) mass-to-charge ratio (m/z) of a particular ion.
A parameter defining the physical units of mass
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.
A material continuant is a real-world object.
A string parameter that contains the URL of a meta-data file.
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]
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.
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.
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.
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.
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]
Describes the molecule, its properties, origin etc. [Dr. York & Satya: 06/13/05]
A parameter describing the identity or a physical property of a molecule. [James & Satya: 04/01/05]
A parameter describing the sequence of residues in a biopolymer. [Dr. York & Satya: 06/28/05]
An individual molecule, categorized according to a few broadly defined classes. [Dr. York & Satya: 06/10/05]
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]
A data collection generated by a mass spectrometer or mass spectral data processing application
A collection of mass spectral data that has been computationally processed - E.G. a peak list [James & Satya: 03/22/05]
A collection of mass spectral data that has NOT been computationally processed other than to change its digital format
A collection of mass spectral data that has NOT been computationally processed, except that it has been converted to mzXML format
A typical mass spectral data pair consisting of a mass-to-charge (m/z) ratio and the abundance associated with that ratio
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]
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.
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.
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.
A solvent molecule that contains carbon, e.g., methanol.
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]
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]
An ion, generated in a mass spectrometer, that is subsequently dissociated into fragment ions in an MS/MS experiment
A human who initiates or implementes a task.
A task that is performed by a human or physical instrument working on a physical sample.
A parameter defining the physical units of a parameter (measurement of setting) [will &satya 04/14/06]
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]
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
A parameter defining the physical units of power
An organism whose cells do not have a nucleus or internal membranes. [Dr. York & Satya: 06/28/05]
A data collection that is classified according to the process that uses/creates/generates it.
A parameter that is classified according to the process that uses/creates/generates it. [will & satya 02/17/06]
The task of processing data using computational applications. [Dr. York & Satya: 11/21/05]
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.
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]
TODO: Find out the various formats, softwares used...
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]
A parameter that specifies the unique identifier for a particular protein in a database. [Dr. York & Satya: 06/13/05]
A protein that catalyzes the cleavage of peptide bonds in proteins to generate peptides. [Dr. York & Satya: 06/28/05]
A molecular aggregate composed of many copies of same molecule. [will & satya 03/02/06]
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).
The computational processing in which a quantity (e.g. amount) is associated with various data elements.
This task converts a raw mass spec data file into the mzXML format.
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]
Tthe physical task of running a mass spectrometer on a specific sample and recording the resulting spectra. [Dr. York & Satya: 11/21/05]
The task of recording raw data using an analytical instrument. [Dr. York & Satya: 11/21/05]
A chemical compound composed of at least one cation (positive ion) and at least one anion (negative ion).
A computational task involving the identification of specific data elements and their replacement by another data element.
The process of separating components by high-performance liquid chromatography.
The process of separating components by chromatography. [Dr. York & Satya: 11/21/05]
Separate components of a mixture by dialysis. The dialysis membrane allows some components to pass through while retaining other components.
Separate components of a mixture by filtration. The filter allows some components to pass through while retaining other components.
The process of separating components by lectin-affinity chromatography.
The process of separating components by size-exclusion chromatography.
The task of physcially spearating the components of a mixture.
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]
The simulation of data from input data. For example, simulation of a theoretical spectrum from a chemical composition. [Dr. York & Satya: 11/21/05]
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]
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]
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.
A small molecule that contains the element carbon.
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]
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]
The solvent of a solution, consisting of many copies of the solvent molecule.
A molecule that exists as a liquid in the laboratory, and that can dissolve other molecules. E.G. water, methanol.
A computational task involving the reordering of data elements according to a specific set of criteria.
A parameter that specifies the cell type from which the biological sample is taken.
A parameter that specifies the organ from which the biological sample is taken.
A parameter that specifies the organism from which the biological sample is taken.
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]
A parameter describing the amount of a substance.
a data collection that describes the physical substances such as buffers, gases etc.
A parameter that identifies a molecule or molecular aggergate.
A parameter that describes a physical substance such as a buffer, gas etc.
A mass spectrometer that can perform both MS and MS/MS analysis. [James & Satya: 03/27/05]
A process that is initiated or implemented by an agent.
A parameter describing the theoretical (calculated) chemical mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05]
A parameter describing the theoretical abundance of a particular ion.
A parameter describing the theoretical charge of a particular ion.
Calculated from the molecular structure. [Dr. York & Satya: 06/28/05]
A parameter describing the theoretical (calculated) mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05]
A parameter describing the theoretical mass-to-charge ratio (m/z) of a particular ion. [will & satya 03/02/06]
A parameter describing the theoretical (calculated) monoisotopic mass of a particular molecule or ion. [Dr. York & Satya: 06/13/05]
A parameter defining the physical units of time
The task of transforming one encoding type into another. For example, binary to ascii. [Dr. York & Satya: 11/21/05]
The transformation of the representational format of data. For example, FASTA format to GCG format. [Dr. York & Satya: 11/21/05]
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]
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]
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]
This describes the tranformation of a given peptide sequence from one format into another. [Dr. York & Satya: 11/21/05]
Class of related proteolytic enzymes that cleave after basic amino acids K & R except when followed by P. [Dr. York & Satya: 06/28/05]
A peptide that is generated by treatment of a protein with the proteolytic enzyme trypsin . [Dr. York & Satya: 06/28/05]
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.
A data collection (in XML format) consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment.
The CAS number of alpha-cyano-4-hydroxycinnamic acid
The CAS number of 2,5-dihydroxybenzoic acid
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.
Defines a matrix composed of 2,5-dihydroxybenzoic acid, used for MALDI MS
A MALDI matrix composed of dihydroxybenzoic acid
An aromatic molecule (2-5-dihydroxybenzoic_acid) used as a MALDI matrix
An aromatic molecule (alpha-cyano-4-hydroxycinnamic acid) used as a MALDI matrix
Defines a matrix composed of alpha-Cyano-4-hydxoxycinnamic_acid, used for MALDI MS
A MALDI matrix composed of alpha-cyano-4-hydroxycinnamic acid
The elementary electrical charge is the charge of a single electron
the physical units of mass in micrograms
the physical units of volume in microliters
the physical units of flowrate in microliters per minute
the physical units of length in micrometers, or 0.000001 meters
the physical units of mass in milligrams
the physical units of volume in milliliters
the physical units of flowrate in milliliters per minute
the physical units of length in millimeters, or 0.001 meters
the physical units of time in milliseconds
The units of electrical potential defined as millivolts, or thousandths of a volt.
the physical units of concentration in moles per liter
the physical units of flowrate in nanoliters per minute
the physical units of length in nanometers, or 0.000000001 meters
The units of electrical potential defined as volts, which can also be expressed as Joules per coulomb
A molecule of water, the most common solvent for HPLC
A collection of water molecules, acting as a solvent
The ChEBI ID of alpha-cyano-4-hydroxycinnamic acid