format-version: 1.4 date: 09:06:2025 14:50 data-version: releases/2025-02-17 saved-by: Deepti Jaiswal Kundu default-namespace: PRIDE namespace-id-rule: * PRIDE:$sequence(7,0,9999999)$ import: http://purl.obolibrary.org/obo/chmo.owl import: http://www.ebi.ac.uk/efo/efo.owl remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ remark: URL: http://purl.obolibrary.org/obo/pride/pride_cv.obo idspace: dce http://purl.org/dc/elements/1.1/ idspace: dcterms http://purl.org/dc/terms/ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# property_value: dce:description "Proteomics Identification Database Ontology, terms describing proteomics data and experimental metadata" xsd:string property_value: dce:title "Proteomics Identification Database Ontology" xsd:string property_value: dce:license https://creativecommons.org/licenses/by/4.0/ property_value: dcterms:license https://creativecommons.org/licenses/by/4.0/ property_value: dce:creator "Deepti Jaiswal Kundu" xsd:string property_value: dce:creator "Nithu Sara John" xsd:string property_value: dce:creator "Yasset Perez-Riverol" xsd:string property_value: dce:homepage https://github.com/PRIDE-Archive/pride-ontology property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000674 property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000828 property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000829 ontology: pride [Term] id: PRIDE:0000000 name: Reference additional parameter def: "Root node for terms relating to Reference additional parameters" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000001 name: Protocol step description additional parameter def: "Root node for terms relating to the description of a protocol as ordered steps" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000002 name: ModificationItem additional parameter def: "Root node for terms relating to the description of a ModificationItem" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000003 name: Peptide item additional parameter def: "Root node for terms relating to the description of a PeptideItem" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000004 name: Identification additional parameter def: "Root node for terms relating to the description of an Identification" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000005 name: Gel additional parameter def: "Root node for terms relating to the description of a Gel parameter" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000006 name: Experiment additional parameter def: "Root node for terms relating to the description of an Experiment" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000007 name: SearchEngineVersion def: "Version number or identifier for search engine"[PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000008 name: Protein search engine output parameter def: "Protein search engine output parameters are critical for analyzing and validating the results of peptide and protein identification" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000009 name: Ion mass tolerance def: "Ion mass tolerence refers to the permissible deviation between the measured mass of an ion and its theoretical mass" [PRIDE:PRIDE] is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000010 name: Precursor ion mass tolerance def: "Precursor ion mass tolerance defines the acceptable range of deviation between the experimental mass-to-charge ratio (𝑚/𝑧)of a precursor ion and its theoretical (m/z) value during database searches" [PRIDE:PRIDE] is_a: PRIDE:0000009 ! Ion mass tolerance [Term] id: PRIDE:0000011 name: MS2 ion mass tolerance def: "MS2 ion mass tolerance refers to the acceptable deviation range between the experimentally measured fragment ion masses and their theoretical values during the identification of peptides and proteins in tandem mass spectrometry (MS/MS)" [PRIDE:PRIDE] is_a: PRIDE:0000009 ! Ion mass tolerance [Term] id: PRIDE:0000012 name: Delta Cn def: "1.0 - normalized correlation score" [PRIDE:PRIDE] is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000045 ! Sequest [Term] id: PRIDE:0000013 name: X correlation def: "A statistical measure used in proteomics to evaluate the quality of peptide-spectrum matches (PSMs) in tandem mass spectrometry (MS/MS) data" [PRIDE:PRIDE] is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000014 name: X correlation (+1) def: "XCorrelation (+1) refers to the cross-correlation score adjustment applied during peptide-spectrum matching (PSM) in search engines like SEQUEST" [PRIDE:PRIDE] is_a: PRIDE:0000013 ! X correlation [Term] id: PRIDE:0000015 name: X correlation (+2) def: "XCorrelation (+2) refers to the cross-correlation (XCorr) scores for peptide-spectrum matches (PSMs) associated with doubly charged precursor ions (𝑧=2) in proteomics" [PRIDE:PRIDE] is_a: PRIDE:0000013 ! X correlation [Term] id: PRIDE:0000016 name: X correlation (+3) def: "XCorrelation (+3) refers to the cross-correlation (XCorr) scores associated with triply charged precursor ions (z=3) in proteomics data analysis" [PRIDE:PRIDE] is_a: PRIDE:0000013 ! X correlation [Term] id: PRIDE:0000017 name: Sample description additional parameter def: "Root term for parameters in the context of ExperimentCollection" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000018 name: Disease free def: "Term to describe the fact that the sample derives from an organism which has been positively shown to be free of disease, e.g. as the consequence of a broad-spectrum screen. NOTE: A request has been made to have this concept added to MeSH. Once this has been achieved, this term will be dropped from the PRIDE CV and all uses of the this term will be updated to the appropriate MeSH concept" [PRIDE:PRIDE] is_a: PRIDE:0000017 ! Sample description additional parameter [Term] id: PRIDE:0000019 name: Solubilization def: "To make something soluble or more soluble, especially in water, by the action of a detergent or other agent" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000020 name: Depletion def: "The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000021 name: Fractionation def: "Process of classification of an analyte or a group of analytes from a sample according to physical (e.g., size) or chemical (e.g., bonding, reactivity) properties. (from https://doi.org/10.1351/goldbook.FT06825)" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000022 name: Separation def: "To separate a complex mixture of proteins or peptides based on molecular characteristics and interaction type over a given amount of time" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000023 name: Band excision def: "The removal of a region of a gel which contains protein(s) of interest" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000024 name: Enzyme digestion def: "The fragmentation of proteins into peptides through the use of an enzyme such as Trypsin" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000025 name: Reduction def: "Reduction generally refers to the chemical process used to break disulfide bonds between cysteine residues in proteins" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000026 name: Alkylation def: "The transfer of an alkyl group from one molecule to another" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000027 name: Mass spectrometry def: "This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000028 name: Cv Label def: "Valid values for cvLabel entries referencing external database or ontology" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000029 name: PubMed def: "PubMed is a free resource developed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM)" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000030 name: PRIDE def: "Valid value for the cvLabel entry referencing PRIDE" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000031 name: GO def: "Valid value for the cvLabel entry referencing GO" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000032 name: MeSH def: "Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH)" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000033 name: NEWT def: "Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000034 name: PSI def: "Valid value for the cvLabel entry referencing the PSI ontology" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000035 name: UNIMOD def: "Valid value for the cvLabel entry referencing UNIMOD" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000036 name: RESID def: "Valid value for the cvLabel entry referencing RESID" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000037 name: Staining def: "A technique used in biology, histology, and microscopy to enhance contrast in samples, making structures or components visible under a microscope" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000038 name: ISBN def: "Valid value for the cvLabel entry referencing ISBN" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000039 name: Organelle isolation def: "Any technique which separates differentiated structures from the cell" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000040 name: Experiment description def: "This CV term should be used in association with a value that is a free-text description of the experiment" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000041 name: Search database protein sequence def: "Database used to search the protein sequence" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000042 name: DOI def: "The DOI system provides a persistent link to the journal's location on the internet, even if the URL changes" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000043 name: FIX def: "Valid value for the cvLabel entry referencing FIX" [PRIDE:PRIDE] is_a: PRIDE:0000028 ! Cv Label [Term] id: PRIDE:0000044 name: Search algorithm def: "A method used to retrieve specific data from a collection of data, based on a given criterion" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000045 name: Sequest def: "Sequest is one of the earliest and most widely used search engines for protein identification in mass spectrometry-based proteomics" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm is_a: PRIDE:0000573 ! Identification software [Term] id: PRIDE:0000046 name: Mascot def: "Mascot is a widely used search engine for protein identification in mass spectrometry-based proteomics" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm is_a: PRIDE:0000571 ! Quantification Software is_a: PRIDE:0000573 ! Identification software [Term] id: PRIDE:0000047 name: X!Tandem def: "X!Tandem is an open-source search engine for protein identification in mass spectrometry-based proteomics" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm is_a: PRIDE:0000573 ! Identification software [Term] id: PRIDE:0000048 name: Output parameter def: "Output parameters in mass spectrometry search engines refer to the results and metrics provided after analyzing the experimental MS/MS spectra and comparing them to theoretical spectra from a protein database" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000049 name: Peptide search engine output parameter def: "The output parameters of a peptide search engine refer to the key metrics, scores, and information that describe the results of matching experimental mass spectra (MS/MS) to theoretical spectra from a protein sequence database" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000050 name: Rank/Sp def: "Final correlation score rank and preliminary score rank" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000045 ! Sequest [Term] id: PRIDE:0000051 name: (M+H)+ def: "M/z of the singly-charged precursor (precursor mass + mass of hydrogen atom)" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000045 ! Sequest [Term] id: PRIDE:0000052 name: Cn def: "Normalized correlation score" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000045 ! Sequest [Term] id: PRIDE:0000053 name: Sequest score def: "Raw correlation score (Sequest)" [PRIDE:PRIDE] is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000045 ! Sequest [Term] id: PRIDE:0000054 name: Sp def: "Preliminary score" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000045 ! Sequest [Term] id: PRIDE:0000055 name: Ions def: "The number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000045 ! Sequest [Term] id: PRIDE:0000056 name: Bioworks def: "A companion tool often used for processing and analyzing mass spectrometry data" [PRIDE:PRIDE] is_a: PRIDE:0000045 ! Sequest is_a: PRIDE:0000573 ! Identification software [Term] id: PRIDE:0000057 name: Molecular weight def: "Molecular weight of a protein" [PRIDE:PRIDE] is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000056 ! Bioworks [Term] id: PRIDE:0000058 name: z score def: "Bioworks z score" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000056 ! Bioworks [Term] id: PRIDE:0000059 name: File def: "File is a digital container used to store information on a computer or other electronic device" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000060 name: Scan def: "The scan refers to a unique identifier for a specific mass spectrum acquired during the experiment. Each scan corresponds to a particular fragmentation event in the mass spectrometer" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000061 name: Coverage def: "Coverage refers to the proportion of a protein sequence that is represented by identified peptides in a given experiment" [PRIDE:PRIDE] is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000056 ! Bioworks [Term] id: PRIDE:0000062 name: rsp def: "It is used as a measure to assess the confidence of peptide identifications based on the output of peptide search engines such as Mascot, SEQUEST, X! Tandem, and others" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000056 ! Bioworks [Term] id: PRIDE:0000063 name: Protein description line def: "A protein description line typically refers to a concise textual entry or annotation that provides information about a specific protein, such as its function, molecular characteristics, or role in biological processes" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000064 name: Secondary accession def: "A secondary accession refers to an additional identifier assigned to a protein entry in databases like UniProt" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000065 name: Upstream flanking sequence def: "Any sequence reported before the start of the peptide" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000066 name: Downstream flanking seqeuence def: "Any sequence reported after the end of the peptide sequence" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000067 name: Reference reporting this experiment def: "Referencing an experiment in scientific contexts, it's important to cite the original publication that reports the methods, results, or analysis involved in the experiment. Typically, this will involve citing the DOI (Digital Object Identifier), journal title, and other relevant details" [PRIDE:PRIDE] is_a: PRIDE:0000000 ! Reference additional parameter [Term] id: PRIDE:0000068 name: Reference describing sample preparation def: "Referencing sample preparation for mass spectrometry or proteomics, the specific protocols and methods can vary depending on the type of analysis being conducted (e.g., quantitative proteomics, post-translational modification analysis, etc.)" [PRIDE:PRIDE] is_a: PRIDE:0000000 ! Reference additional parameter [Term] id: PRIDE:0000069 name: Mascot score def: "Score as defined for the Mascot search algorithm" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000046 ! Mascot [Term] id: PRIDE:0000070 name: Peptide cleavage def: "Cleavage of the peptide bond" [PRIDE:PRIDE] is_a: PRIDE:0000024 ! Enzyme digestion [Term] id: PRIDE:0000071 name: Search engine setting def: "Search engine settings refer to the specific parameters and configurations that are used to optimize how a peptide or protein search engine identifies and matches experimental data (e.g., MS/MS spectra) to theoretical peptide sequences in a database" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000072 name: Fixed modification setting def: "Fixed modifications refer to chemical modifications that are consistently present in all peptides of a given experiment, typically due to a sample preparation step or reagent used" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000073 name: Variable modification setting def: "Variable modifications refer to post-translational modifications (PTMs) or other chemical changes that can occur at specific amino acid residues but do not necessarily occur in every peptide or protein" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000074 name: Maximum Missed Cleavages Setting def: "The maximum missed cleavages setting refers to the number of missed enzyme cleavages allowed during peptide digestion" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000075 name: Mass value type setting def: "It refers to how the mass of peptides, ions, or proteins is represented during a search or analysis" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000076 name: Mass value type setting monoisotopic def: "The monoisotopic mass setting refers to the mass of a molecule based on the lightest isotope of each element, typically the most abundant isotope, like carbon-12 (12C) for carbon, hydrogen-1 (1H) for hydrogen, and oxygen-16 (16O) for oxygen" [PRIDE:PRIDE] is_a: PRIDE:0000075 ! Mass value type setting [Term] id: PRIDE:0000077 name: Mass value type setting average def: "The average mass setting refers to the weighted average mass of all isotopes of each element present in a molecule" [PRIDE:PRIDE] is_a: PRIDE:0000075 ! Mass value type setting [Term] id: PRIDE:0000078 name: Peptide mass tolerance setting def: "The peptide mass tolerance setting is a critical parameter used to define how much variation is acceptable between the observed mass of a peptide in the mass spectrum and the theoretical mass calculated from a database search" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000079 name: Accurate mass mode setting def: "The Accurate Mass Mode setting refers to a mode of operation where the mass spectrometer is configured to measure the mass of ions with a higher degree of precision than in standard scanning modes" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000080 name: Accurate mass mode setting true def: "Accurate mass mode setting typically refers to configuring the instrument to measure ion masses with high precision" [PRIDE:PRIDE] is_a: PRIDE:0000079 ! Accurate mass mode setting [Term] id: PRIDE:0000081 name: Accurate mass mode setting false def: "Accurate mass mode setting is set to false in mass spectrometry, it means that the instrument will not prioritize high-resolution mass measurements" [PRIDE:PRIDE] is_a: PRIDE:0000079 ! Accurate mass mode setting [Term] id: PRIDE:0000082 name: Mass error type setting def: "The mass error type setting refers to how mass errors are reported and interpreted during data acquisition and analysis" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000083 name: mass error type setting ppm def: "The mass error type is set to ppm (parts per million), it specifies that the acceptable mass error is calculated relative to the theoretical mass of the ion, and it is expressed as parts per million (ppm)" [PRIDE:PRIDE] is_a: PRIDE:0000082 ! Mass error type setting [Term] id: PRIDE:0000084 name: mass error type setting mmu def: "Mass errors refer to discrepancies in the measured mass of ions compared to their theoretical or expected mass values" [PRIDE:PRIDE] is_a: PRIDE:0000082 ! Mass error type setting [Term] id: PRIDE:0000085 name: mass error type setting percent def: "Mass error type setting percent refers to the percentage of mass error in the measured mass-to-charge ratio (m/z) compared to the expected or theoretical value" [PRIDE:PRIDE] is_a: PRIDE:0000082 ! Mass error type setting [Term] id: PRIDE:0000086 name: mass error type setting Daltons def: "Mass error type daltons, how the discrepancy between the measured and expected mass is expressed in absolute units of mass (daltons), rather than as a percentage" [PRIDE:PRIDE] is_a: PRIDE:0000082 ! Mass error type setting [Term] id: PRIDE:0000087 name: Protonated setting def: "Protonated setting refers to the protonation of a molecule or ion during the ionization process, particularly in positive ion mode" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000088 name: Protonated setting MH+ def: "Protonated setting MH⁺ refers to the protonated molecular ion of a compound, where M represents the neutral molecule, and the H⁺ signifies the added proton" [PRIDE;PRIDE] is_a: PRIDE:0000087 ! Protonated setting [Term] id: PRIDE:0000090 name: Protonated setting M-H- def: "Protonated setting M-H⁻ refers to the deprotonated molecular ion (also known as the negative ion form), where M represents the neutral molecule, and H⁻ signifies the loss of a proton (H⁺), resulting in a negatively charged ion" [PRIDE:PRIDE] is_a: PRIDE:0000087 ! Protonated setting [Term] id: PRIDE:0000091 name: Rank def: "Rank represents the quality or confidence of the peptide-spectrum match (PSM), with the rank value showing the best match and progressively lower-ranked results indicating less confident identifications" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000092 name: All peptides matched def: "The output of a peptide search engine where every peptide in a sample has been identified and matched against a database" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000093 name: All peptides matched true def: "All peptides matched true is in a peptide search engine output (like Mascot, SEQUEST, X! Tandem, or Andromeda), it generally means that all detected peptide spectra were successfully matched to corresponding peptides in the protein database" [PRIDE:PRIDE] is_a: PRIDE:0000092 ! All peptides matched [Term] id: PRIDE:0000094 name: All peptides matched false def: "Some mass spectra from the experiment could not be linked to a known peptide sequence from the protein database" [PRIDE:PRIDE] is_a: PRIDE:0000092 ! All peptides matched [Term] id: PRIDE:0000095 name: Masses matched def: "Masses matched refers to the number (or percentage) of experimental mass-to-charge ratios (m/z) from a mass spectrum that were successfully matched to theoretical peptide masses in a protein database" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000096 name: Reported Chromosome def: "Reported chromosome is the chromosomal location of the protein or peptide that has been identified" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000097 name: Project def: "Allows experiments to be grouped or organised under projects. Experiments may be grouped under more than one project" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000098 name: Indistinguishable alternative protein accession def: "A qualifier is mandatory when using this term. The qualifier is an alternative protein accession that is indistinguishable from the primary protein accession based upon observed peptide sequences only" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000099 name: PeptideProphet probability score def: "The probability score for this peptide assignment to be correct, as calculated by PeptideProphet" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000101 ! PeptideProphet [Term] id: PRIDE:0000100 name: ProteinProphet probability score def: "The probability score for this protein identification to be correct, as calculated by ProteinProphet" [PRIDE:PRIDE] is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000102 ! ProteinProphet [Term] id: PRIDE:0000101 name: PeptideProphet def: "The PeptideProphet algorithm" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm [Term] id: PRIDE:0000102 name: ProteinProphet def: "The ProteinProphet algorithm" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm [Term] id: PRIDE:0000103 name: Gel run date def: "The date upon which the gel was run. A value is mandatory - must be formatted as xsd:dateTime" [PRIDE:PRIDE] is_a: PRIDE:0000005 ! Gel additional parameter [Term] id: PRIDE:0000104 name: Sample volume loaded def: "The volume of sample loaded on to the gel measured in micro litres. Mandatory value must be formatted as xsd:Double" [PRIDE:PRIDE] is_a: PRIDE:0000005 ! Gel additional parameter [Term] id: PRIDE:0000105 name: Width in pixels def: "The width of the referenced gel image in pixels. Mandatory value of type xsd:int" [PRIDE:PRIDE] is_a: PRIDE:0000005 ! Gel additional parameter [Term] id: PRIDE:0000106 name: Height in pixels def: "The height of the referenced gel image in pixels. Mandatory value of type xsd:int" [PRIDE:PRIDE] is_a: PRIDE:0000005 ! Gel additional parameter [Term] id: PRIDE:0000107 name: Gel spot parameter def: "Parameters describing the spot on a gel that has been analysed resulting in the annotated protein identification" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000108 name: Gel spot intensity def: "The intensity of the spot on the gel. Mandatory value of type xsd:double" [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter [Term] id: PRIDE:0000109 name: Gel spot area def: "The area of the spot on the gel measured in millimetres squared. Mandatory value of type xsd:double" [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter [Term] id: PRIDE:0000110 name: Gel spot volume def: "The volume of the spot on the gel measured in millimetres cubed. Mandatory value of type xsd:double" [PRIDE:PRIDE] is_a: PRIDE:0000131 ! Spot normalized volume [Term] id: PRIDE:0000111 name: Reference describing data analysis def: "A reference annotated with this term describes analysis of the data presented in the enclosing PRIDE experiment" [PRIDE:PRIDE] is_a: PRIDE:0000000 ! Reference additional parameter [Term] id: PRIDE:0000112 name: Identified by peptide mass fingerprint def: "The annotated protein identification arises from peptide mass fingerprinting. Peptide identifications may or may not be included" [PRIDE:PRIDE] synonym: "PMF" EXACT [PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000113 name: Identified by peptide fragmentation def: "The protein identification annotated with this term has been identified by peptide fragmentation and subsequent database searching" [PRIDE:PRIDE] synonym: "PFF" EXACT [PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000114 name: iTRAQ reagent 114 def: "The name of the sample labelled with iTRAQ reagent 114" [PRIDE:PRIDE] is_a: PRIDE:0000329 ! iTRAQ reagent [Term] id: PRIDE:0000115 name: iTRAQ reagent 115 def: "The name of the sample labelled with iTRAQ reagent 115" [PRIDE:PRIDE] is_a: PRIDE:0000329 ! iTRAQ reagent [Term] id: PRIDE:0000116 name: iTRAQ reagent 116 def: "The name of the sample labelled with iTRAQ reagent 116" [PRIDE:PRIDE] is_a: PRIDE:0000329 ! iTRAQ reagent [Term] id: PRIDE:0000117 name: iTRAQ reagent 117 def: "The name of the sample labelled with iTRAQ reagent 117" [PRIDE:PRIDE] is_a: PRIDE:0000329 ! iTRAQ reagent [Term] id: PRIDE:0000118 name: iTRAQ intensity 114 def: "The intensity of the sample labelled with iTRAQ reagent 114" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000119 name: iTRAQ intensity 115 def: "The intensity of the sample labelled with iTRAQ reagent 115" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000120 name: iTRAQ intensity 116 def: "The intensity of the sample labelled with iTRAQ reagent 116" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000121 name: iTRAQ intensity 117 def: "The intensity of the sample labelled with iTRAQ reagent 117" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000122 name: Two Dimensional Polyacrylamide Gel Electrophoresis def: "A type of gel electrophoresis in which proteins are first separated by charge and then by molecular weight, enabling the analysis of complex protein mixtures" [PRIDE:PRIDE] is_a: PRIDE:0000022 ! Separation [Term] id: PRIDE:0000123 name: Immobilized pH Gradient Electrophoresis def: "Electrophoresis using an gel which has a pH gradient along its length" [PRIDE:PRIDE] is_a: PRIDE:0000122 ! Two Dimensional Polyacrylamide Gel Electrophoresis is_a: PRIDE:0000568 ! 2D PAGE [Term] id: PRIDE:0000124 name: Sodium dodecyl sulfate polyacrylamide gel electrophoresis def: "A type of polyacrylamide gel electrophoresis in which the anionic detergent sodium dodecyl sulfate (SDS) is used to denature the sample proteins into linear monomers, rendering their charge proportional to their length so that migration is a function of size. Abbreviated SDS-polyacrylamide gel electrophoresis or SDS-PAGE" [PRIDE:PRIDE] is_a: PRIDE:0000122 ! Two Dimensional Polyacrylamide Gel Electrophoresis is_a: PRIDE:0000568 ! 2D PAGE [Term] id: PRIDE:0000125 name: pH low value def: "The lowest pH of an immobilised pH gradient gel" [PRIDE:PRIDE] is_a: PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis [Term] id: PRIDE:0000126 name: pH high value def: "The highest pH of an immobilised pH gradient gel" [PRIDE:PRIDE] is_a: PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis [Term] id: PRIDE:0000127 name: IPG strip length cm def: "The length in centimeters of an immobilised pH gradient gel" [PRIDE:PRIDE] is_a: PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis [Term] id: PRIDE:0000128 name: First dimension details def: "Details of immobilised pH gradient gel electrophoresis which exclude the pH range of the gel and strip length parameters" [PRIDE:PRIDE] is_a: PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis [Term] id: PRIDE:0000129 name: Second dimension details def: "Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis" [PRIDE:PRIDE] is_a: PRIDE:0000124 ! Sodium dodecyl sulfate polyacrylamide gel electrophoresis [Term] id: PRIDE:0000131 name: Spot normalized volume def: "A value for spot volume which is standardized across gels and is derived from the individual gel spot volume values" [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter [Term] id: PRIDE:0000132 name: Spot normalized volume method def: "The method by which the normalized value for spot volume is derived from the individual gel spot volume values" [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter [Term] id: PRIDE:0000133 name: Isobaric residue K/Q def: "The amino acids glutamine (Q) (mol wt = 146) cannot be distinguished from lysine (K) (mol wt = 146)" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000134 name: Anticoagulant def: "A substance that prevents coagulation; that is, it stops blood from clotting" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000135 name: Mapping date def: "Date of last mapping of given identifier to current UniProt accession number" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000136 name: Mapping status def: "Status of last mapping of given identifier to current UniProt accession number. Valid values are 'mappingAllOK', 'not mapped peptide mismatch', 'not mapped accession not found' and 'not mapped taxon not found'" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000137 name: Mapping history def: "Status of last mapping of given identifier to current UniProt accession number. Valid values are 'unchanged since last mapping', 'changed accession' and 'changed version of accession'" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000138 name: Discriminant score def: "PeptideProphet discriminant score fval" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000101 ! PeptideProphet [Term] id: PRIDE:0000139 name: Not Mapped SOAP Error def: "Error message: SOAP protocol failed" [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status [Term] id: PRIDE:0000140 name: Not Mapped Database Error def: "Error message: Error with queried database" [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status [Term] id: PRIDE:0000141 name: Not Mapped No Mapping Found def: "Error message: Unable to match given identifier" [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status [Term] id: PRIDE:0000142 name: Not Mapped Peptide Mismatch def: "Error message: One or more peptide sequences did not match query sequence" [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status [Term] id: PRIDE:0000143 name: Mapped Taxon Not Found def: "Error message: No mapping to proteins from defined taxon" [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status [Term] id: PRIDE:0000144 name: Mapped All Ok def: "Sucessful completion of operation message" [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status [Term] id: PRIDE:0000145 name: PepSplice def: "The PepSplice algorithm" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm is_a: PRIDE:0000573 ! Identification software [Term] id: PRIDE:0000146 name: PepSplice precision def: "PepSplice precision refers to the accuracy of peptide-spectrum matches (PSMs) produced by the PepSplice search engine, a specialized tool used for the identification of peptides, particularly for novel or unexpected peptide sequences. Precision is a key metric used to assess the quality and reliability of search results in proteomics" [PRIDE:PRIDE] is_a: PRIDE:0000145 ! PepSplice is_a: PRIDE:0000145 ! PepSplice [Term] id: PRIDE:0000147 name: PepSplice false discovery rate def: "PepSlice false discovery rate is a critical metric used to control the number of false positives (incorrect peptide-spectrum matches or PSMs) in the search results" [PRIDE:PRIDE] is_a: PRIDE:0000145 ! PepSplice is_a: PRIDE:0000145 ! PepSplice [Term] id: PRIDE:0000148 name: PepSplice P-value def: "A Score based on the hypergeometric model" [PRIDE:PRIDE] is_a: PRIDE:0000145 ! PepSplice is_a: PRIDE:0000145 ! PepSplice [Term] id: PRIDE:0000149 name: PepSplice Deltascore def: "The Difference between the pvalues of the 1st and the 2nd best peptide; if two peptides have the same pvalue, they are taken together" [PRIDE:PRIDE] is_a: PRIDE:0000145 ! PepSplice is_a: PRIDE:0000145 ! PepSplice [Term] id: PRIDE:0000150 name: PepSplice Score Count def: "The score count" [PRIDE:PRIDE] is_a: PRIDE:0000145 ! PepSplice is_a: PRIDE:0000145 ! PepSplice [Term] id: PRIDE:0000151 name: PepSplice Penalty def: "The Sum of all penalties for the peptide assignment" [PRIDE:PRIDE] is_a: PRIDE:0000145 ! PepSplice is_a: PRIDE:0000145 ! PepSplice [Term] id: PRIDE:0000152 name: PepSplice Read Direction def: "The reading direction on the DNA" [PRIDE:PRIDE] is_a: PRIDE:0000145 ! PepSplice is_a: PRIDE:0000145 ! PepSplice [Term] id: PRIDE:0000153 name: PepSplice Forward Read Direction def: "The reading direction on the DNA is 5' to 3'" [PRIDE:PRIDE] is_a: PRIDE:0000152 ! PepSplice Read Direction [Term] id: PRIDE:0000154 name: PepSplice Reverse Read Direction def: "The reading direction on the DNA 3' to 5'" [PRIDE:PRIDE] is_a: PRIDE:0000152 ! PepSplice Read Direction is_a: PRIDE:0000145 ! PepSplice [Term] id: PRIDE:0000155 name: Unmappable def: "Unsucessful mapping" [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status [Term] id: PRIDE:0000156 name: Project identifier def: "Unique identifier of project" [PRIDE:PRIDE] synonym: "Project Identifier" EXACT [NCIT] is_a: PRIDE:0000097 ! Project [Term] id: PRIDE:0000157 name: Search type def: "Type of search" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000158 name: MS search def: "It refers to the process of identifying and characterizing molecules, especially proteins, peptides, metabolites, and small molecules, using mass spectrometry (MS) data" [PRIDE:PRIDE] is_a: PRIDE:0000157 ! Search type [Term] id: PRIDE:0000159 name: MS/MS search def: "MS/MS Search refers to the process of identifying molecules (typically proteins, peptides, metabolites, or small molecules) using tandem mass spectrometry (MS/MS) data. Unlike simple mass spectrometry (MS1), MS/MS involves fragmenting precursor ions into smaller product ions, generating a detailed fragmentation pattern or spectra that can be used to identify the structure or sequence of the molecule" [PRIDE:PRIDE] is_a: PRIDE:0000157 ! Search type [Term] id: PRIDE:0000160 name: Enzyme def: "Type of enzyme used to fragment the protein. The value will equal the name of the enxzyme used e.g" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000161 name: Fragment mass tolerance setting def: "Range of acceptable fragment masses accepted by instrument" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000162 name: Allowed missed cleavages def: "Number of missed cleavage sites taken into account" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000163 name: Instrument type def: "Name of instrument used in analysis" [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting [Term] id: PRIDE:0000164 name: Mapped Without Supporting Peptides def: "Sucessful mapping without supporting evidence from peptides" [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status [Term] id: PRIDE:0000165 name: Automatic allocation def: "PICR tool has allocated the accession number" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000166 name: Ambiguous modification def: "Modification with a MonoDeltaMass, which can not unambiguously be assigned to only one modification and for which several possibilities exist" [PRIDE:PRIDE] is_a: PRIDE:0000002 ! ModificationItem additional parameter [Term] id: PRIDE:0000167 name: Novel locus information def: "Detailed information about a genomic locus identified by whole genome searches" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000168 name: Nucleic acid sequence def: "A nucleic acid sequence refers to the linear arrangement of nucleotides (the basic building blocks of DNA and RNA) in a specific order" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000169 name: Start position of the nucleic acid sequence on the chromosome def: "The start position of a nucleic acid sequence on a chromosome refers to the location or coordinate where the sequence begins within the linear structure of a chromosome" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000170 name: Stop position of the nucleic acid sequence on the chromosome def: "The stop position of a nucleic acid sequence on a chromosome refers to the ending coordinate where the sequence finishes on the chromosome" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000171 name: funding reference def: "A funding reference is a formal acknowledgment of financial support provided by an organization, institution, or agency for a research project, study, or publication" [PRIDE:PRIDE] is_a: PRIDE:0000000 ! Reference additional parameter [Term] id: PRIDE:0000172 name: Search database protein sequence length def: "Value of average of all individual peptide identifications for this protein" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000173 name: MeanOfPeptideScores def: "Value of average of all individual peptide scores" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000174 name: Isoelectric point def: "Isoelectric point of a protein" [PRIDE:PRIDE] synonym: "pI" EXACT [PRIDE] is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000056 ! Bioworks [Term] id: PRIDE:0000175 name: XML generation software def: "The software which was used to generate the PRIDE XML file" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000176 name: X\!Tandem Hyperscore def: "The X!Tandem hyperscore for the peptide" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000177 name: Spectrum Mill peptide score def: "The Spectrum Mill score for the peptide" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000178 name: Peptide selection def: "A protocol step to select for a particular type of peptides" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000179 name: dotproduct def: "X|Tandem dot product score" [PRIDE:PRIDE] is_a: PRIDE:0000047 ! X|Tandem [Term] id: PRIDE:0000180 name: delta def: "X|Tandem delta score" [PRIDE:PRIDE] is_a: PRIDE:0000047 ! X|Tandem [Term] id: PRIDE:0000181 name: deltastar def: "X|Tandem delta star score" [PRIDE:PRIDE] is_a: PRIDE:0000047 ! X|Tandem [Term] id: PRIDE:0000182 name: zscore def: "X|Tandem Z score" [PRIDE:PRIDE] is_a: PRIDE:0000047 ! X|Tandem [Term] id: PRIDE:0000183 name: expect def: "X|Tandem expectancy score" [PRIDE:PRIDE] is_a: PRIDE:0000047 ! X|Tandem [Term] id: PRIDE:0000184 name: Query number def: "Search parameter that allows users to find query results from old data" [PRIDE:PRIDE] is_a: PRIDE:0000046 ! Mascot [Term] id: PRIDE:0000185 name: OMSSA E-value def: "E-value parameter from OMSSA" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000186 name: OMSSA P-value def: "P-value parameter from OMSSA" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000187 name: Fragment Ion Annotation def: "Fragment ion annotation of the peptide" [PRIDE:PRIDE] synonym: "Product ion property" EXACT [PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000188 name: product ion m/z def: "Mass" [PRIDE:PRIDE] synonym: "Fragment ion mass" EXACT [PRIDE] is_a: PRIDE:0000187 ! Fragment Ion Annotation [Term] id: PRIDE:0000189 name: product ion intensity def: "Intensity" [PRIDE] synonym: "Fragment ion intensity" EXACT [PRIDE] is_a: PRIDE:0000187 ! Fragment Ion Annotation [Term] id: PRIDE:0000190 name: product ion mass error def: "Mass error" [PRIDE:PRIDE] synonym: "Fragment ion mass error" EXACT [PRIDE] is_a: PRIDE:0000187 ! Fragment Ion Annotation [Term] id: PRIDE:0000191 name: product ion retention time error def: "Product ion retention time error in minutes" [PRIDE:PRIDE] synonym: "Fragment ion retention time error" EXACT [PRIDE] is_a: PRIDE:0000187 ! Fragment Ion Annotation [Term] id: PRIDE:0000192 name: product ion type def: "Product ion type" [PRIDE:PRIDE] synonym: "Fragment ion type" EXACT [PRIDE] is_a: PRIDE:0000187 ! Fragment Ion Annotation [Term] id: PRIDE:0000193 name: y ion def: "Y ion type" [PRIDE:PRIDE] synonym: "y fragment ion" EXACT [PRIDE] is_a: PRIDE:0000192 ! product ion type [Term] id: PRIDE:0000194 name: b ion def: "B ion type" [PRIDE:PRIDE] synonym: "b fragment ion" EXACT [PRIDE] is_a: PRIDE:0000192 ! product ion type [Term] id: PRIDE:0000195 name: b ion -NH3 def: "B ion type with a neutral loss of an ammonia group" [PRIDE:PRIDE] synonym: "b fragment ion -NH3" EXACT [PRIDE] is_a: PRIDE:0000194 ! b ion [Term] id: PRIDE:0000196 name: b ion -H2O def: "B ion type with a neutral loss of a water molecule" [PRIDE:PRIDE] synonym: "b fragment ion -H2O" EXACT [PRIDE] is_a: PRIDE:0000194 ! b ion [Term] id: PRIDE:0000197 name: y ion -H2O def: "Y ion type with the neutral loss of a molecule water" [PRIDE:PRIDE] synonym: "y fragment ion -H2O" EXACT [PRIDE] is_a: PRIDE:0000193 ! y ion [Term] id: PRIDE:0000198 name: y ion -NH3 def: "Y ion type with the neutral loss of an ammonia group" [PRIDE:PRIDE] synonym: "y fragment ion -NH3" EXACT [PRIDE] is_a: PRIDE:0000193 ! y ion [Term] id: PRIDE:0000199 name: in source ion def: "Ion resulting from in-source fragmentation" [PRIDE:PRIDE] synonym: "In source fragment ion" EXACT [PRIDE] synonym: "In-source ion" EXACT [PRIDE] is_a: PRIDE:0000192 ! product ion type [Term] id: PRIDE:0000200 name: non-identified ion def: "Fragment ion that could not be assigned to a predicted fragment ion mass" [PRIDE:PRIDE] synonym: "unidentified ion" EXACT [PRIDE] is_a: PRIDE:0000192 ! product ion type [Term] id: PRIDE:0000201 name: co-eluting ion def: "Fragment ion that was matched to another, co-eluting peptide precursor" [PRIDE:PRIDE] is_a: PRIDE:0000192 ! product ion type [Term] id: PRIDE:0000202 name: Parent Ion Annotation def: "Parent ion annotation of the peptide" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000203 name: parent ion retention time def: "Retention time in minutes" [PRIDE:PRIDE] is_a: PRIDE:0000202 ! Parent Ion Annotation [Term] id: PRIDE:0000204 name: product ion charge def: "Charge state" [PRIDE:PRIDE] synonym: "Fragment ion charge" EXACT [PRIDE] is_a: PRIDE:0000187 ! Fragment Ion Annotation [Term] id: PRIDE:0000205 name: Heavy stable isotope label def: "A general term for any stable isotope method" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000206 name: Heavy stable isotope label residue def: "Heavy stable isotope label residue" [PRIDE:PRIDE] is_a: PRIDE:0000205 ! Heavy stable isotope label [Term] id: PRIDE:0000207 name: Light stable isotope label def: "Light stable isotope label" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000208 name: Light stable isotope label residue def: "The precise amino acid that has been modified" [PRIDE:PRIDE] is_a: PRIDE:0000207 ! Light stable isotope label [Term] id: PRIDE:0000209 name: Peptide pair id def: "Facilitate mapping between peptide pairs (usually heavy/light) to which the stable isotope ratio below relates" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000210 name: Stable isotope ratio def: "Ratio of peptide pair the sequence/sample is the numerator in the ratio" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000211 name: Quantitative sample reference def: "This links back to the value given to the heavy/light stable isotope label to relate the peptide ratio back to the sample" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000212 name: Mascot expect value def: "Expect value as defined for the Mascot search algorithm" [PRIDE:PRIDE] is_a: PRIDE:0000046 ! Mascot [Term] id: PRIDE:0000213 name: Inspect def: "The Inspect search algorithm" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm is_a: PRIDE:0000573 ! Identification software [Term] id: PRIDE:0000214 name: Inspect MQScore def: "Quality score of a match" [PRIDE:PRIDE] is_a: PRIDE:0000213 ! Inspect [Term] id: PRIDE:0000215 name: Inspect p-value def: "Probability that the top match is correct" [PRIDE:PRIDE] is_a: PRIDE:0000213 ! Inspect [Term] id: PRIDE:0000216 name: ProteomExchange project accession number def: "ProteomExchange accession number of the project where the PRIDE experiment is included" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000217 name: ProteomExchange project hash def: "Hash in Tranche of the whole ProteomExchange project where the PRIDE experiment is included" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000218 name: Original MS data file format def: "Original format of the file containing MS data" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000219 name: Date of search def: "Date when the search was performed" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000220 name: Calculated Mass To Charge Ratio def: "M/z value converted from the MH+ value, according to this formula: CalculatedMZ = (precursorMH+ - HYDROGEN_MASS + (precursorCharge * HYDROGEN_MASS))/ precursorCharge" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000221 name: parent ion retention time error def: "Parent retention time error in minutes" [PRIDE:PRIDE] is_a: PRIDE:0000202 ! Parent Ion Annotation [Term] id: PRIDE:0000227 name: x ion def: "X ion type" [PRIDE:PRIDE] synonym: "x fragment ion" EXACT [PRIDE] is_a: PRIDE:0000192 ! product ion type [Term] id: PRIDE:0000228 name: x ion -H2O def: "X ion type with the neutral loss of a molecule water" [PRIDE:PRIDE] synonym: "x fragment ion -H2O" EXACT [PRIDE] is_a: PRIDE:0000227 ! x ion [Term] id: PRIDE:0000229 name: x ion -NH3 def: "X ion type with the neutral loss of an ammonia group" [PRIDE:PRIDE] synonym: "x fragment ion -NH3" EXACT [PRIDE] is_a: PRIDE:0000227 ! x ion [Term] id: PRIDE:0000230 name: z ion def: "Z ion type" [PRIDE:PRIDE] synonym: "z fragment ion" EXACT [PRIDE] is_a: PRIDE:0000192 ! product ion type [Term] id: PRIDE:0000231 name: z ion -H2O def: "Z ion type with the neutral loss of a molecule water" [PRIDE:PRIDE] synonym: "z fragment ion -H2O" EXACT [PRIDE] is_a: PRIDE:0000230 ! z ion [Term] id: PRIDE:0000232 name: z ion -NH3 def: "Z ion type with the neutral loss of an ammonia group" [PRIDE:PRIDE] synonym: "z fragment ion -NH3" EXACT [PRIDE] is_a: PRIDE:0000230 ! z ion [Term] id: PRIDE:0000233 name: a ion def: "A ion type" [PRIDE:PRIDE] synonym: "a fragment ion" EXACT [PRIDE] is_a: PRIDE:0000192 ! product ion type [Term] id: PRIDE:0000234 name: a ion -H2O def: "A ion type with the neutral loss of a molecule water" [PRIDE:PRIDE] synonym: "a fragment ion -H2O" EXACT [PRIDE] is_a: PRIDE:0000233 ! a ion [Term] id: PRIDE:0000235 name: a ion -NH3 def: "A ion type with the neutral loss of an ammonia group" [PRIDE:PRIDE] synonym: "A fragment ion -NH3" EXACT [PRIDE] is_a: PRIDE:0000233 ! a ion [Term] id: PRIDE:0000236 name: c ion def: "C ion type" [PRIDE:PRIDE] synonym: "c fragment ion" EXACT [PRIDE] is_a: PRIDE:0000192 ! product ion type [Term] id: PRIDE:0000237 name: c ion -H2O def: "C ion type with the neutral loss of a molecule water" [PRIDE:PRIDE] synonym: "c fragment ion -H2O" EXACT [PRIDE] is_a: PRIDE:0000236 ! c ion [Term] id: PRIDE:0000238 name: c ion -NH3 def: "C ion type with the neutral loss of an ammonia group" [PRIDE:PRIDE] synonym: "c fragment ion -NH3" EXACT [PRIDE] is_a: PRIDE:0000236 ! c ion [Term] id: PRIDE:0000239 name: immonium ion def: "Immonium ion type" [PRIDE:PRIDE] is_a: PRIDE:0000192 ! product ion type [Term] id: PRIDE:0000240 name: immonium A def: "Immonium ion type for alanine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000241 name: immonium C def: "Immonium ion type for cysteine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000242 name: immonium D def: "Immonium ion type for aspartic acid" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000243 name: immonium E def: "Immonium ion type for glutamic acid" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000244 name: immonium F def: "Immonium ion type for phenylalanine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000245 name: immonium G def: "Immonium ion type for glycine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000246 name: immonium H def: "Immonium ion type for histidine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000247 name: immonium I def: "Immonium ion type for isoleucine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000248 name: immonium K def: "Immonium ion type for lysine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000249 name: immonium L def: "Immonium ion type for leucine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000250 name: immonium M def: "Immonium ion type for methionine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000251 name: immonium N def: "Immonium ion type for asparagine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000252 name: immonium P def: "Immonium ion type for proline" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000253 name: immonium Q def: "Immonium ion type for glutamine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000254 name: immonium R def: "Immonium ion type for arginine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000255 name: immonium S def: "Immonium ion type for serine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000256 name: immonium T def: "Immonium ion type for threnine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000257 name: immonium V def: "Immonium ion type for valine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000258 name: immonium W def: "Immonium ion type for tryptophan" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000259 name: immonium Y def: "Immonium ion type for tyrosine" [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion [Term] id: PRIDE:0000260 name: precursor ion type def: "Precursor ion type" [PRIDE:PRIDE] synonym: "Parent ion type" EXACT [PRIDE] is_a: PRIDE:0000202 ! Parent Ion Annotation [Term] id: PRIDE:0000261 name: precursor ion -H2O def: "Precursor ion type with the neutral loss of a molecule water" [PRIDE:PRIDE] synonym: "Parent ion -H2O" EXACT [PRIDE] is_a: PRIDE:0000263 ! precursor ion [Term] id: PRIDE:0000262 name: precursor ion -NH3 def: "Precursor ion type with the neutral loss of an ammonia group" [PRIDE:PRIDE] synonym: "Parent ion -NH3" EXACT [PRIDE] is_a: PRIDE:0000263 ! precursor ion [Term] id: PRIDE:0000263 name: precursor ion def: "Precursor ion" [PRIDE:PRIDE] synonym: "Parent ion" EXACT [PRIDE] is_a: PRIDE:0000260 ! precursor ion type [Term] id: PRIDE:0000264 name: iTRAQ reagent 113 def: "The name of the sample labelled with iTRAQ reagent 113" [PRIDE:PRIDE] is_a: PRIDE:0000329 ! iTRAQ reagent [Term] id: PRIDE:0000265 name: iTRAQ reagent 118 def: "The name of the sample labelled with iTRAQ reagent 118" [PRIDE:PRIDE] is_a: PRIDE:0000329 ! iTRAQ reagent [Term] id: PRIDE:0000266 name: iTRAQ reagent 119 def: "The name of the sample labelled with iTRAQ reagent 119" [PRIDE:PRIDE] is_a: PRIDE:0000329 ! iTRAQ reagent [Term] id: PRIDE:0000267 name: iTRAQ reagent 121 def: "The name of the sample labelled with iTRAQ reagent 121" [PRIDE:PRIDE] is_a: PRIDE:0000329 ! iTRAQ reagent [Term] id: PRIDE:0000268 name: iTRAQ intensity 113 def: "The intensity of the sample labelled with iTRAQ reagent 113" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000269 name: iTRAQ intensity 118 def: "The intensity of the sample labelled with iTRAQ reagent 118" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000270 name: iTRAQ intensity 119 def: "The intensity of the sample labelled with iTRAQ reagent 119" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000271 name: iTRAQ intensity 121 def: "The intensity of the sample labelled with iTRAQ reagent 121" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000272 name: Project secondary name def: "Allows experiments inside the same project to be grouped or organised as subprojects. This will not be displayed in the PRIDE web page" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000273 name: SloMo score threshold for valid modification location def: "The SloMo score threshold for a valid modification location is a statistical cutoff used in mass spectrometry (MS/MS) to determine the confidence that a specific position within a peptide or protein is modified" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm [Term] id: PRIDE:0000274 name: MaxQuant percentage threshold for valid modification location def: "In MaxQuant, the percentage threshold for a valid modification location is typically based on the site probability for post-translational modification (PTM) localization. This probability indicates the confidence that a particular amino acid (residue) within a peptide is modified" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm [Term] id: PRIDE:0000275 name: SloMo score def: "The SloMo score is a quantitative measure used in mass spectrometry (MS/MS) for the localization of modification sites within a peptide or protein sequence" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm [Term] id: PRIDE:0000276 name: MaxQuant percentage def: "It refers to typically relates to the localization probability of a post-translational modification (PTM) on a peptide" [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm [Term] id: PRIDE:0000277 name: Valid location def: "A valid location refers to a site on a peptide or protein sequence that has been confidently identified as being modified" [PRIDE:PRIDE] is_a: PRIDE:0000002 ! ModificationItem additional parameter [Term] id: PRIDE:0000278 name: Processing method additional parameter def: "A processing method refers to the specific steps or algorithms used to analyze raw MS data, identify peptides, and assign modifications. These processing methods often come with additional parameters that allow users to customize the analysis based on their experimental needs" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000279 name: In silico enzyme digestion def: "Enzyme that is selected as a parameter of the search engine" [PRIDE:PRIDE] is_a: PRIDE:0000278 ! Processing method additional parameter [Term] id: PRIDE:0000280 name: zH ion def: "Z ion type with one extra proton" [PRIDE:PRIDE] synonym: "zH fragment ion" EXACT [PRIDE] is_a: PRIDE:0000230 ! z ion [Term] id: PRIDE:0000281 name: zHH ion def: "Z ion type with two extra protons" [PRIDE:PRIDE] synonym: "zHH fragment ion" EXACT [PRIDE] is_a: PRIDE:0000230 ! z ion [Term] id: PRIDE:0000282 name: Fixed modification def: "Fixed type of post-translational modification" [PRIDE:PRIDE] is_a: PRIDE:0000002 ! ModificationItem additional parameter [Term] id: PRIDE:0000283 name: Variable modification def: "Variable type of post-translational modification" [PRIDE:PRIDE] is_a: PRIDE:0000002 ! ModificationItem additional parameter [Term] id: PRIDE:0000284 name: Sf def: "The Sf score for each peptide is calculated by a neural network algorithm that incorporates teh Xcorr, DeltaCn, Sp, RSp, peptide mass, charge state, and the number of matched peptides for the search. The protein Sf score is the sum of peptide Sf scores for all the peptides associated with that protein" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter is_a: PRIDE:0000045 ! Sequest [Term] id: PRIDE:0000285 name: TMT reagent 126 def: "The name of the sample labelled with TMT reagent 126" [PRIDE:PRIDE] is_a: PRIDE:0000337 ! TMT reagent [Term] id: PRIDE:0000286 name: TMT reagent 127 def: "The name of the sample labelled with TMT reagent 127" [PRIDE:PRIDE] is_a: PRIDE:0000337 ! TMT reagent [Term] id: PRIDE:0000287 name: TMT reagent 128 def: "The name of the sample labelled with TMT reagent 128" [PRIDE:PRIDE] is_a: PRIDE:0000337 ! TMT reagent [Term] id: PRIDE:0000288 name: TMT reagent 129 def: "The name of the sample labelled with TMT reagent 129" [PRIDE:PRIDE] is_a: PRIDE:0000337 ! TMT reagent [Term] id: PRIDE:0000289 name: TMT reagent 130 def: "The name of the sample labelled with TMT reagent 130" [PRIDE:PRIDE] is_a: PRIDE:0000337 ! TMT reagent [Term] id: PRIDE:0000290 name: TMT reagent 131 def: "The name of the sample labelled with TMT reagent 131" [PRIDE:PRIDE] is_a: PRIDE:0000337 ! TMT reagent [Term] id: PRIDE:0000291 name: TMT intensity 126 def: "The intensity value of the sample labelled with TMT reagent 126 [Curator:ACSORDAS]" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000292 name: TMT intensity 127 def: "The intensity value of the sample labelled with TMT reagent 127 [Curator:ACSORDAS]" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000293 name: TMT intensity 128 def: "The intensity value of the sample labelled with TMT reagent 128 [Curator:ACSORDAS]" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000294 name: TMT intensity 129 def: "The intensity value of the sample labelled with TMT reagent 129 [Curator:ACSORDAS]" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000295 name: TMT intensity 130 def: "The intensity value of the sample labelled with TMT reagent 130 [Curator:ACSORDAS]" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000296 name: TMT intensity 131 def: "The intensity value of the sample labelled with TMT reagent 131 [Curator:ACSORDAS]" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000297 name: Gene name def: "Name of the gene that has been identified (if a nucleotide database was used to perform the search)" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000298 name: Modification Position in Protein Sequence def: "Position of the modification in the protein sequence" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000299 name: Submitted Protein Accession def: "The original submitted protein accession for this identification. This might have been curated as part of the submission process" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000300 name: Gel spot identifier def: "The gel spot's identifier. This identifier should resemble the one used in, for example, the associated publication" [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter [Term] id: PRIDE:0000301 name: Non-significant protein identification def: "Identifies a protein identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value)" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000302 name: Non-significant peptide identification def: "Identifies a peptide identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value)" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000303 name: Decoy hit def: "Indicates that this protein identification comes from the used decoy database" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000304 name: Gel identifier def: "The gel's identifier. This identifier should resemble the one used in, for example, the associated publication" [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter [Term] id: PRIDE:0000305 name: Gel-based experiment def: "Defines a gel-based proteomics experiment" [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics [Term] id: PRIDE:0000306 name: Imported from NCBI Peptidome def: "It refers to the process of retrieving peptide data from the NCBI Peptidome database for use in various proteomics analyses" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000307 name: Quantification method def: "Defines various quantification methods" [PRIDE:PRIDE] is_a: PRIDE:0000391 ! Quantification parameter [Term] id: PRIDE:0000308 name: Gel-based quantification method def: "Describes gel-based quantification methods" [PRIDE:PRIDE] is_a: PRIDE:0000307 ! Quantification method [Term] id: PRIDE:0000309 name: Gel-free quantification method def: "Describes gel-free quantification methods" [PRIDE:PRIDE] is_a: PRIDE:0000307 ! Quantification method [Term] id: PRIDE:0000310 name: Isotope labeling def: "Describes quantification techniques using isotope labeling" [PRIDE:PRIDE] is_a: PRIDE:0000309 ! Gel-free quantification method [Term] id: PRIDE:0000311 name: Selected Reaction Monitoring def: "Describes quantification techniques based on selected / multiple reaction monitoring" [PRIDE:PRIDE] is_a: PRIDE:0000309 ! Gel-free quantification method [Term] id: PRIDE:0000312 name: Label free def: "Describes label free quantification techniques" [PRIDE:PRIDE] is_a: PRIDE:0000309 ! Gel-free quantification method [Term] id: PRIDE:0000313 name: iTRAQ def: "Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level" [PRIDE:PRIDE] is_a: PRIDE:0000317 ! MS2 based isotope labeling [Term] id: PRIDE:0000314 name: TMT def: "Tandem Mass Tag is a MS2 based isotope labeling quantification technique" [PRIDE:PRIDE] synonym: "Tandem Mass Tag" EXACT [PRIDE] is_a: PRIDE:0000317 ! MS2 based isotope labeling is_a: PRIDE:0000514 ! Quantification channel label [Term] id: PRIDE:0000315 name: SILAC def: "Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification" [PRIDE:PRIDE] synonym: "Stable isotope labeling with amino acids in cell culture" EXACT [PRIDE] is_a: PRIDE:0000316 ! MS1 based isotope labeling is_a: PRIDE:0000514 ! Quantification channel label [Term] id: PRIDE:0000316 name: MS1 based isotope labeling def: "Describes isotope labeling quantification techniques detectable at MS1 level" [PRIDE:PRIDE] is_a: PRIDE:0000310 ! Isotope labeling [Term] id: PRIDE:0000317 name: MS2 based isotope labeling def: "Describes isotope labeling quantification techniques detectable at MS2 level" [PRIDE:PRIDE] is_a: PRIDE:0000310 ! Isotope labeling [Term] id: PRIDE:0000318 name: 18O def: "The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen" [PRIDE:PRIDE] is_a: PRIDE:0000316 ! MS1 based isotope labeling is_a: PRIDE:0000597 ! metabolic label [Term] id: PRIDE:0000319 name: ICAT def: "Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements" [PRIDE:PRIDE] synonym: "Isotope-Coded Affinity Tags" EXACT [PRIDE] is_a: PRIDE:0000316 ! MS1 based isotope labeling is_a: PRIDE:0000514 ! Quantification channel label [Term] id: PRIDE:0000320 name: AQUA def: "AQUA is an isotope labeling based quantification technique that uses known peptides" [PRIDE:PRIDE] is_a: PRIDE:0000316 ! MS1 based isotope labeling [Term] id: PRIDE:0000321 name: ICPL def: "Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses" [PRIDE:PRIDE] synonym: "Isotope-coded protein label" EXACT [PRIDE] is_a: PRIDE:0000316 ! MS1 based isotope labeling [Term] id: PRIDE:0000322 name: emPAI def: "The Exponentially Modified Protein Abundance Index (emPAI) offers approximate, label-free, relative quantification of the proteins in a mixture based on protein coverage by the peptide matches in a database search result" [PRIDE:PRIDE] synonym: "Exponentially Modified Protein Abundance Index" EXACT [PRIDE] is_a: PRIDE:0000312 ! Label free [Term] id: PRIDE:0000323 name: TIC def: "The Total Ion Current (TIC) can be measured or calculated in order to target specific ions" [PRIDE:PRIDE] synonym: "Total Ion Current" EXACT [PRIDE] is_a: PRIDE:0000312 ! Label free [Term] id: PRIDE:0000324 name: Quantification reagent def: "A reagent used for quantification" [PRIDE:PRIDE] is_a: PRIDE:0000017 ! Sample description additional parameter is_a: PRIDE:0000391 ! Quantification parameter [Term] id: PRIDE:0000325 name: SILAC heavy def: "The heavy label used in SILAC experiments" [PRIDE:PRIDE] is_a: PRIDE:0000328 ! SILAC reagent is_a: PRIDE:0000315 ! SILAC [Term] id: PRIDE:0000326 name: SILAC light def: "The light reagent used in SILAC experiments" [PRIDE:PRIDE] is_a: PRIDE:0000328 ! SILAC reagent is_a: PRIDE:0000315 ! SILAC [Term] id: PRIDE:0000327 name: SILAC medium def: "The medium weight reagent used in SILAC experiments" [PRIDE:PRIDE] is_a: PRIDE:0000328 ! SILAC reagent is_a: PRIDE:0000315 ! SILAC [Term] id: PRIDE:0000328 name: SILAC reagent def: "Reagent used in SILAC labeling" [PRIDE:PRIDE] is_a: PRIDE:0000433 ! Reagents used in Labeled Method [Term] id: PRIDE:0000329 name: iTRAQ reagent def: "Reagent used in iTRAQ experiments" [PRIDE:PRIDE] is_a: PRIDE:0000433 ! Reagents used in Labeled Method [Term] id: PRIDE:0000330 name: Arbitrary quantification unit def: "A unit describing values that can only be interpreted within the same spectrum but cannot be compared to values found in other spectra and or experiments" [PRIDE:PRIDE] is_a: PRIDE:0000392 ! Quantification unit [Term] id: PRIDE:0000331 name: Counts def: "Quantification values reported as arbitrary counts (most often ion counts)" [PRIDE:PRIDE] is_a: PRIDE:0000330 ! Arbitrary quantification unit [Term] id: PRIDE:0000337 name: TMT reagent def: "Reagent used in TMT experiments" [PRIDE:PRIDE] is_a: PRIDE:0000433 ! Reagents used in Labeled Method [Term] id: PRIDE:0000344 name: ICAT reagent def: "Reagent used in ICAT experiments" [PRIDE:PRIDE] is_a: PRIDE:0000433 ! Reagents used in Labeled Method [Term] id: PRIDE:0000345 name: ICAT light reagent def: "The ICAT light reagent is a chemical reagent that labels proteins for comparison with heavy reagents" [PRIDE:PRIDE] is_a: PRIDE:0000344 ! ICAT reagent [Term] id: PRIDE:0000346 name: ICAT heavy reagent def: "The ICAT heavy reagent is a chemical reagent used to label proteins for protein profiling" [PRIDE:PRIDE] is_a: PRIDE:0000344 ! ICAT reagent [Term] id: PRIDE:0000347 name: ICPL reagent def: "Reagent used in ICPL experiments" [PRIDE:PRIDE] is_a: PRIDE:0000433 ! Reagents used in Labeled Method [Term] id: PRIDE:0000348 name: ICPL 0 reagent def: "ICPL_0 reagent is a crucial component in the ICPL methodology, serving as the light isotopic label that provides a reference point for quantitative proteomic analyses" [PRIDE:PRIDE] is_a: PRIDE:0000347 ! ICPL reagent [Term] id: PRIDE:0000349 name: ICPL 4 reagent def: "ICPLn4 reagent is a specific labeling compound that incorporates four deuterium (^2H) atoms, resulting in a mass shift of approximately 4.0251 Da per labeled amino acid compared to the light ICPL_0 reagent" [PRIDE:PRIDE] is_a: PRIDE:0000347 ! ICPL reagent [Term] id: PRIDE:0000350 name: ICPL 6 reagent def: "The ICPL 6 reagent is a labeling compounds, designed to introduce a mass shift of approximately 6.0204 Da per labeled amino group" [PRIDE:PRIDE] is_a: PRIDE:0000347 ! ICPL reagent [Term] id: PRIDE:0000351 name: ICPL 10 reagent def: "The ICPL 10 reagent is a labeling compounds, designed to introduce a mass shift of approximately 10 Da per labeled amino group" [PRIDE:PRIDE] is_a: PRIDE:0000347 ! ICPL reagent [Term] id: PRIDE:0000352 name: Quantification value def: "Parameters to report quantification values"[PRIDE:PRIDE] is_a: PRIDE:0000391 ! Quantification parameter [Term] id: PRIDE:0000353 name: Multiplexed quantification value def: "Parameters describing quantification values for multiplexed samples" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter is_a: PRIDE:0000352 ! Quantification value [Term] id: PRIDE:0000354 name: Intensity subsample 1 def: "Intensity subsampling 1 typically refers to selecting first subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE] is_a: PRIDE:0000353 ! Multiplexed quantification value [Term] id: PRIDE:0000355 name: Intensity subsample 2 def: "Intensity subsampling 2 typically refers to selecting second subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE] is_a: PRIDE:0000353 ! Multiplexed quantification value [Term] id: PRIDE:0000356 name: Intensity subsample 3 def: "Intensity subsampling 3 typically refers to selecting third subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE] is_a: PRIDE:0000353 ! Multiplexed quantification value [Term] id: PRIDE:0000357 name: Intensity subsample 4 def: "Intensity subsampling 4 typically refers to selecting fourth subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE] is_a: PRIDE:0000353 ! Multiplexed quantification value [Term] id: PRIDE:0000358 name: Intensity subsample 5 def: "Intensity subsampling 5 typically refers to selecting fifth subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE] is_a: PRIDE:0000353 ! Multiplexed quantification value [Term] id: PRIDE:0000359 name: Intensity subsample 6 def: "Intensity subsampling 6 typically refers to selecting sixth subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE] is_a: PRIDE:0000353 ! Multiplexed quantification value [Term] id: PRIDE:0000360 name: Intensity subsample 7 def: "Intensity subsampling 7 typically refers to selecting seventh subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE] is_a: PRIDE:0000353 ! Multiplexed quantification value [Term] id: PRIDE:0000361 name: Intensity subsample 8 def: "Intensity subsampling 8 typically refers to selecting eighth subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE] is_a: PRIDE:0000353 ! Multiplexed quantification value [Term] id: PRIDE:0000362 name: Other quantification value def: "Values from other quantification techniques" [PRIDE:PRIDE] is_a: PRIDE:0000352 ! Quantification value [Term] id: PRIDE:0000363 name: emPAI value def: "The emPAI for the protein" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter is_a: PRIDE:0000362 ! Other quantification value [Term] id: PRIDE:0000364 name: TIC value def: "The Total Ion Count for the given entity" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter is_a: PRIDE:0000362 ! Other quantification value [Term] id: PRIDE:0000365 name: Multiplexed sample description def: "Describes multiples subsamples" [PRIDE:PRIDE] is_a: PRIDE:0000017 ! Sample description additional parameter [Term] id: PRIDE:0000366 name: Contains multiple subsamples def: "Identifies samples that are made up of multiplexed subsamples" [PRIDE:PRIDE] is_a: PRIDE:0000365 ! Multiplexed sample description [Term] id: PRIDE:0000391 name: Quantification parameter def: "Quantification related parameter" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000392 name: Quantification unit def: "Unit used to report quantification results" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter is_a: PRIDE:0000391 ! Quantification parameter [Term] id: PRIDE:0000393 name: Relative quantification unit def: "Unit to report relative quantification results" [PRIDE:PRIDE] is_a: PRIDE:0000392 ! Quantification unit [Term] id: PRIDE:0000394 name: Absolute quantification unit def: "Unit used to describe absolute quantification results" [PRIDE:PRIDE] is_a: PRIDE:0000392 ! Quantification unit [Term] id: PRIDE:0000395 name: Ratio def: "Quantification results represent ratios" [PRIDE:PRIDE] is_a: PRIDE:0000393 ! Relative quantification unit [Term] id: PRIDE:0000396 name: Copies per cell def: "Quantification results are reported as copies per cell" [PRIDE:PRIDE] is_a: PRIDE:0000394 ! Absolute quantification unit [Term] id: PRIDE:0000397 name: Data derived from previous dataset def: "One dataset is a reanalysis of previously published data" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000398 name: No PTMs are included in the dataset def: "No post-translational-modifications are been included in the identified peptides of one dataset" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000399 name: Accepted manuscript def: "A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000400 name: Reference xref: value-type:xsd\:string "The allowed value-type for this CV term" def: "Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000401 name: Experimental information has been refined since this experiment was originally made publicly available def: "This means that the experimental information available has been improved, for instance precursor charges were added" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000402 name: Original data def: "A dataset is not a reanalysis of previously published data" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000403 name: Associated file URI def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000404 name: Associated raw file URI def: "URI of a raw data file associated to the PRIDE experiment (maybe through a PX submission)" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000403 ! Associated file URI is_a: PRIDE:0000577 ! file uri [Term] id: PRIDE:0000405 name: Submit PRIDE Experiment to IntAct def: "Indicates that this PRIDE experiment contains interaction data and should be submitted to IntAct (maybe through a PX submission)" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000406 name: ProteomeCentral dataset URI def: "URI associated to one PX submission in ProteomeCentral" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000407 name: Result file URI def: "URI of one file labeled as 'Result', associated to one PX submission" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000403 ! Associated file URI is_a: PRIDE:0000577 ! file uri [Term] id: PRIDE:0000408 name: Search engine output file URI def: "URI of one search engine output file associated to one PX submission" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000403 ! Associated file URI is_a: PRIDE:0000577 ! file uri [Term] id: PRIDE:0000409 name: Peak list file URI def: "URI of one of one search engine output file associated to one PX submission" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000403 ! Associated file URI is_a: PRIDE:0000577 ! file uri [Term] id: PRIDE:0000410 name: 'Other' type file URI def: "URI of one file labeled as 'Other', associated to one PX submission" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000403 ! Associated file URI is_a: PRIDE:0000577 ! file uri [Term] id: PRIDE:0000411 name: Dataset FTP location def: "FTP location of one entire PX data set" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000412 name: Dataset with no associated published manuscript def: "A dataset which does not have an associated published manuscript" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000413 name: Instrument name def: "The value of this term (related to one PRIDE experiment) can be used to provide the name of instruments that are not included in any other CV yet" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000414 name: Peer-reviewed dataset def: "Dataset has been peer-reviewed somehow" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000415 name: Non peer-reviewed dataset def: "Dataset that has not been peer-reviewed by any means" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000416 name: Supported dataset by repository def: "The PX dataset is supported by and is available through the submission repository" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000417 name: Unsupported dataset by repository def: "The PX dataset is not fully supported by the submission repository" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000418 name: Other member of protein ambiguity group def: "Accession of another protein that was assigned to the same protein ambiguity group. This term must be repeated to include all protein group members, except for itself" [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter [Term] id: PRIDE:0000419 name: b ion -H3PO4 def: "B ion type with a neutral loss of a phosphate molecule" [PRIDE:PRIDE] synonym: "B fragment ion -H3PO4" EXACT [PRIDE] is_a: PRIDE:0000194 ! b ion [Term] id: PRIDE:0000420 name: b ion -2H3PO4 def: "B ion type with a neutral loss of 2 phosphate molecules" [PRIDE:PRIDE] synonym: "B fragment ion -2H3PO4" EXACT [PRIDE] is_a: PRIDE:0000194 ! b ion [Term] id: PRIDE:0000421 name: b ion -3H3PO4 def: "B ion type with a neutral loss of 3 phosphate molecules" [PRIDE:PRIDE] synonym: "B fragment ion -3H3PO4" EXACT [PRIDE] is_a: PRIDE:0000194 ! b ion [Term] id: PRIDE:0000422 name: y ion -H3PO4 def: "Y ion type with a neutral loss of a phosphate molecule" [PRIDE:PRIDE] synonym: "y fragment ion -H3PO4" EXACT [PRIDE] is_a: PRIDE:0000193 ! y ion [Term] id: PRIDE:0000423 name: y ion -2H3PO4 def: "Y ion type with a neutral loss of 2 phosphate molecules" [PRIDE:PRIDE] synonym: "y fragment ion -2H3PO4" EXACT [PRIDE] is_a: PRIDE:0000193 ! y ion [Term] id: PRIDE:0000424 name: y ion -3H3PO4 def: "Y ion type with a neutral loss of 3 phosphate molecules" [PRIDE:PRIDE] synonym: "y fragment ion -3H3PO4" EXACT [PRIDE] is_a: PRIDE:0000193 ! y ion [Term] id: PRIDE:0000425 name: MS1 intensity based label-free quantification method def: "A a widely used approach in mass spectrometry-based proteomics for quantifying protein abundances across different samples" [PRIDE:PRIDE] is_a: PRIDE:0000309 ! Gel-free quantification method [Term] id: PRIDE:0000426 name: Mass spectrometry proteomics experimental strategy def: "The basic mass spectrometry strategy used in the experiment" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000427 name: Top-down proteomics def: "A mass spectrometry-based approach that analyzes intact proteins rather than digesting them into peptides (as in bottom-up proteomics)" [PRIDE:PRIDE] is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000428 name: Bottom-up proteomics def: "Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer" [PRIDE:PRIDE] is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000429 name: MS/MS shotgun proteomics def: "Bottom-up MS/MS shotgun experiment with data-dependent acquisition, using nomenclature in PMID 20622845, the method of choice for the a priori identification of the protein components of complex samples" [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics [Term] id: PRIDE:0000430 name: Chemical cross-linking coupled with mass spectrometry proteomics def: "Chemical cross-linking of proteins coupled with mass spectrometry analysis to provide information about protein folding and protein-protein interaction" [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics [Term] id: PRIDE:0000431 name: Affinity purification coupled with mass spectrometry proteomics def: "Affinity purification combined with mass spectrometry (AP-MS) has been used to understand protein-complex composition and protein-protein interaction" [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics [Term] id: PRIDE:0000432 name: Dataset with its publication pending def: "A dataset which has an associated manuscript pending for publication" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000433 name: Reagents used in Labeled Methods def: "Labeled reagents used for quantification" [PRIDE:PRIDE] is_a: PRIDE:0000324 ! Quantification reagent [Term] id: PRIDE:0000434 name: Unlabeled sample def: "An unlabeled sample used for quantification" [PRIDE:PRIDE] is_a: PRIDE:0000324 ! Quantification reagent [Term] id: PRIDE:0000435 name: Peptide counting def: "Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140" [PRIDE:PRIDE] is_a: PRIDE:0000312 ! Label free [Term] id: PRIDE:0000436 name: Spectrum counting def: "Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140" [PRIDE:PRIDE] is_a: PRIDE:0000312 ! Label free [Term] id: PRIDE:0000437 name: PAI def: "Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140" [PRIDE:PRIDE] is_a: PRIDE:0000312 ! Label free [Term] id: PRIDE:0000438 name: Spectrum count/molecular weight def: "Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140" [PRIDE:PRIDE] is_a: PRIDE:0000312 ! Label free [Term] id: PRIDE:0000439 name: SAF def: "The spectrum count is normalized for protein length. Method reviewed in PMID 22772140" [PRIDE:PRIDE] is_a: PRIDE:0000312 ! Label free [Term] id: PRIDE:0000440 name: NSAF def: "Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140" [PRIDE:PRIDE] is_a: PRIDE:0000312 ! Label free [Term] id: PRIDE:0000441 name: APEX - Absolute Protein Expression def: "Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140" [PRIDE:PRIDE] is_a: PRIDE:0000312 ! Label free [Term] id: PRIDE:0000442 name: Tissue not applicable to dataset def: "Tissue not applicable to dataset" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000443 name: Original NCBI Peptidome submission files def: "The NCBI FTP location of the original Sample - Experiment level Peptidome submission data" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000444 name: PRIDE experiment accession def: "Accession number of a given PRIDE experiment (called assay in the PRIDE-3 system)" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000445 name: PRIDE Cluster score def: "It is an integer that gives an indication about the quality of a peptide spectrum match in PRIDE-Q. It uses the PRIDE-Cluster algorithm (described in PMID: 23361086) and different criteria to assign it (number of spectra in a cluster, ratio of the predominant peptide identification in the cluster, etc)" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000446 name: PRIDE peptide score def: "Score used in PRIDE-Q to give an indication of the quality of a peptide spectrum match. It is described in PMID:16964243" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000447 name: SWATH MS def: "ABsciex Data Independent Acquisition method that consists of unfractionated samples acquisition by using duty cycles adapted to HPLC chromatography, acquiring sequential wide fragment ions spectra, typically covering the precursor mass space from 400 m/z to 1200 m/z on each duty cycle. Acquired data is interrogated by using libraries of peptide coordinates (normalised elution time, fragment ion masses and intensities). It is described in PMID:22261725" [PRIDE:PRIDE] is_a: PRIDE:0000450 ! Data-independent acquisition [Term] id: PRIDE:0000448 name: Additional associated raw file URI def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000403 ! Associated file URI is_a: PRIDE:0000577 ! file uri [Term] id: PRIDE:0000449 name: Gel image file URI def: "URI of one gel image file associated to one PX submission" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000403 ! Associated file URI is_a: PRIDE:0000577 ! file uri [Term] id: PRIDE:0000450 name: Data-independent acquisition def: "Predefined m/z ranges are interrogated either by fragmenting all ions entering the mass spectrometer at every single point in chromatographic time; or by dividing the m/z range into smaller m/z ranges for isolation and fragmentation. See review in PMID:24281846" [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics is_a: PRIDE:0000659 ! Proteomics data acquisition method [Term] id: PRIDE:0000451 name: MSE def: "Waters data independent acquisition method based on UPLC chromatography and MS acquisition of cycles of two spectra, in low and high energy respectively, in a QQ-TOF instrument. It is described in PMID: 16755610" [PRIDE:PRIDE] is_a: PRIDE:0000450 ! Data-independent acquisition [Term] id: PRIDE:0000452 name: HDMSE def: "Waters data independent acquisition method, which consists of using an additional on-line separation dimension (Ion Mobility drift) and an MSE acquisition. It is described in PMID: 22811061" [PRIDE:PRIDE] is_a: PRIDE:0000450 ! Data-independent acquisition [Term] id: PRIDE:0000453 name: PAcIFIC def: "Precursor Acquisition Independent From Ion Count. A Data Independent Acquisition method performed in ion traps that consists of the acquisition of 2.5 m/z width sequential windows over several injections of the same material, until a precursor m/z range of about 400 to 1200 m/z is covered. It is described in PMID: 21341720" [PRIDE:PRIDE] is_a: PRIDE:0000450 ! Data-independent acquisition [Term] id: PRIDE:0000454 name: All-ion fragmentation def: "MS Data Independent Acquisition performed in Thermo Orbitrap instruments. It consists of the acquisition of cycles of two spectra, a precursor mass MS1 spectrum, and a fragment ions MS2 spectrum where a wide mass filter (typically over 800 m/z) is applied to the precursors. It is described in PMID: 20610777" [PRIDE:PRIDE] is_a: PRIDE:0000450 ! Data-independent acquisition [Term] id: PRIDE:0000455 name: Protein-protein cross-linking experiment def: "Protein-protein cross-linking experiment to provide information about protein folding and protein-protein interaction" [PRIDE:PRIDE] is_a: PRIDE:0000430 ! Chemical cross-linking coupled with mass spectrometry proteomics [Term] id: PRIDE:0000456 name: Protein-RNA cross-linking experiment def: "Protein-RNA cross-linking experiment to provide information about Protein-RNA interaction" [PRIDE:PRIDE] is_a: PRIDE:0000430 ! Chemical cross-linking coupled with mass spectrometry proteomics [Term] id: PRIDE:0000457 name: Experiment Type def: "Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000458 name: Metaproteomics def: "Studying all protein samples of diverse host environments like the human body, soil or sea water" [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type synonym: "Community Proteomics" EXACT [PRIDE] synonym: "Environmental Proteomics" RELATED [PRIDE:PRIDE] [Term] id: PRIDE:0000459 name: Human Metaproteomics def: "Investigating both human host proteins and associated microbial proteins at the same time from human samples" [PRIDE:PRIDE] is_a: PRIDE:0000458 ! Metaproteomics [Term] id: PRIDE:0000460 name: Proteogenomics def: "Studies that use proteomic information to improve genome annotation. Proteogenomics approaches are also increasingly used in personalised medicine studies" [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000461 name: Multi-omics study def: "Studies that use various omics methods like proteomics, genomics, transcriptomics, metabolomics to analyse the same biological samples" [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000462 name: SONAR def: "Waters data independent acquisition method" [PRIDE:PRIDE] is_a: PRIDE:0000450 ! Data-independent acquisition [Term] id: PRIDE:0000463 name: PRM def: "Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis" [PRIDE:PRIDE] is_a: PRIDE:0000311 ! Selected Reaction Monitoring [Term] id: PRIDE:0000464 name: Fasta file URI def: "URI of one external Fasta file associated to the PRIDE experiment (maybe through a PX submission)" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000465 name: Spectral Library file URI def: "URI of one external Spectral Library file associated to the PRIDE experiment (maybe through a PX submission)" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000466 name: Quantification result file URI def: "URI of one external Quantification file associated to the PRIDE experiment (maybe through a PX submission)" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000467 name: MS Image file URI def: "URI of one external Mass spectrometry Image file associated to the PRIDE experiment (maybe through a PX submission)" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000468 name: Aspera Protocol def: "URI for an Aspera Download Protocol" [PRIDE:PRIDE] xref: value-type:xsd\:string "The allowed value-type for this CV term" is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000469 name: FTP Protocol def: "URI for an FTP Download Protocol" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000470 name: File Properties def: "PRIDE File Properties for all type of files" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000471 name: MS File Properties def: "Properties for MS , Peaks files" [PRIDE:PRIDE] is_a: PRIDE:0000470 ! File Properties [Term] id: PRIDE:0000472 name: MS min charge def: "Minimum charge for all precursor in the file" [PRIDE:PRIDE] is_a: PRIDE:0000471 ! MS File Properties [Term] id: PRIDE:0000473 name: MS max charge def: "Maximum charge for all precursor in the file" [PRIDE:PRIDE] is_a: PRIDE:0000471 ! MS File Properties [Term] id: PRIDE:0000474 name: MS min RT def: "Minimum retention time in the File" [PRIDE:PRIDE] is_a: PRIDE:0000471 ! MS File Properties [Term] id: PRIDE:0000475 name: MS max RT def: "Maximum retention time in the file" [PRIDE:PRIDE] is_a: PRIDE:0000471 ! MS File Properties [Term] id: PRIDE:0000476 name: MS min MZ def: "Minimum precursor mass to charge in the file" [PRIDE:PRIDE] is_a: PRIDE:0000471 ! MS File Properties [Term] id: PRIDE:0000477 name: MS max MZ def: "Maximum precursor mass to charge in the file" [PRIDE:PRIDE] is_a: PRIDE:0000471 ! MS File Properties [Term] id: PRIDE:0000478 name: Number of scans def: "Total number of scans in the file" [PRIDE:PRIDE] is_a: PRIDE:0000471 ! MS File Properties [Term] id: PRIDE:0000479 name: MS scan range def: "Range of scan number in the ms file" [PRIDE:PRIDE] is_a: PRIDE:0000471 ! File Properties [Term] id: PRIDE:0000480 name: Number of MS def: "Number of MS in the file" [PRIDE:PRIDE] is_a: PRIDE:0000471 ! MS File Properties [Term] id: PRIDE:0000481 name: Number of MS1 spectra def: "Number of MS1 spectra" [PRIDE:PRIDE] is_a: PRIDE:0000480 ! Number of MS [Term] id: PRIDE:0000482 name: Number of MS2 spectra def: "Number of MS2 spectra in the file" [PRIDE:PRIDE] is_a: PRIDE:0000480 ! Number of MS [Term] id: PRIDE:0000483 name: Number of MS3 spectra def: "Total number of MS3 spectra in the file" [PRIDE:PRIDE] is_a: PRIDE:0000480 ! Number of MS [Term] id: NCIT:C69199 name: Content Creation date def: "The date on which data creation began [NCI]" [PRIDE:PRIDE] is_a: PRIDE:0000470 ! File Properties [Term] id: PRIDE:0000484 name: Result analysis parameters def: "The result analysis parameters is a term to group all the parameters for proteomics data analysis" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000485 name: Global result parameters def: "Result analysis parameters share by multiple search engine and Quantiative tools" [PRIDE:PRIDE] is_a: PRIDE:0000484 ! Result analysis parameters [Term] id: PRIDE:0000486 name: Tool specific analysis parameters def: "Result analysis parameters specific to a search engine or quantitative tool" [PRIDE:PRIDE] is_a: PRIDE:0000484 ! Result analysis parameters [Term] id: PRIDE:0000487 name: Min charge def: "Minimum charge of precursor to be search" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000488 name: Max charge def: "Maximum charge of precursor to be search" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000489 name: Min RT def: "Min Retention time for precursor to be search" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000490 name: Max RT def: "Maximum precursor RT to be search" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000491 name: Number of missed cleavages def: "Number of missed cleavages" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000492 name: Max peptide AA length def: "Max peptide amino acid length for search" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000493 name: Min peptide AA length def: "Minimum peptide amino acid length for search" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000494 name: Min precursor MZ def: "Min precursor MZ (mass) for precursor to search" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000495 name: Max precursor MZ def: "Max precursor MZ (mass) for precursor to search" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000496 name: Min peak length def: "Min number of peaks in the spectrum to be search" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000497 name: Use Multi Modification def: "Use Multi Modification"[PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000498 name: Use Additional Variable Modifications def: "Use Additional Variable Modifications" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000499 name: Do Mass Filtering def: "Do Mass Filtering" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000500 name: Intensity Threshold def: "Intensity Threshold" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000501 name: Max Labeled AA def: "Max Labeled AA" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000502 name: Max Number of Modifications (PTMs) def: "Max Number of Modifications (PTMs)" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000503 name: First Search Precursor Tolerance def: "First Search Precursor Tolerance" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000504 name: Main Search Precursor Tolerance def: "Main Search Precursor Tolerance" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000505 name: Individual Accession def: "Accession or Code of the individual in the sample" [PRIDE:PRIDE] is_a: PRIDE:0000017 ! Sample description additional parameter [Term] id: PRIDE:0000506 name: Number identified proteins def: "Total number of reported proteins. This property can be used to report the number of proteins identified in an Assay or experiment" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000507 name: Number of identified peptides def: "Total number of identified peptides in an experiment or assay" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000508 name: Number of modified peptides def: "The total number of peptides identified with post-translational modifications" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000509 name: Number of PSMs def: "Total number of reported identified Peptide Spectrum matches (PSMs)" [PRIDE:PRIDE] is_a: PRIDE:0000485 ! Global result parameters [Term] id: PRIDE:0000510 name: File size def: "The size of the file in MB" [PRIDE:PRIDE] is_a: PRIDE:0000470 ! File Properties [Term] id: PRIDE:0000511 name: Pass submitter threshold def: "Pass submitter threshold" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000512 name: RNA mass spectrometry def: "RNA mass spectrometry" [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics [Term] id: PRIDE:0000513 name: Dimethyl Labeling def: "Dimethyl Labeling (DML)" [PRIDE:PRIDE] is_a: PRIDE:0000310 ! Isotope labeling [Term] id: PRIDE:0000514 name: Label def: "Quantification channel label" [PRIDE:PRIDE] is_a: PRIDE:0000017 ! Sample description additional parameter [Term] id: PRIDE:0000516 name: TMT126 def: "TMT126" [PRIDE:PRIDE] is_a: PRIDE:0000666 ! TMT6PLEX is_a: PRIDE:0000667 ! TMT10PLEX is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000517 name: TMT127 def: "TMT127" [PRIDE:PRIDE] is_a: PRIDE:0000666 ! TMT6PLEX [Term] id: PRIDE:0000518 name: TMT127C def: "TMT127C" [PRIDE:PRIDE] is_a: PRIDE:0000667 ! TMT10PLEX is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000519 name: TMT127N def: "TMT127N" [PRIDE:PRIDE] is_a: PRIDE:0000667 ! TMT10PLEX is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000520 name: TMT128 def: "TMT128" [PRIDE:PRIDE] is_a: PRIDE:0000666 ! TMT6PLEX [Term] id: PRIDE:0000521 name: TMT128C def: "TMT128C" [PRIDE:PRIDE] is_a: PRIDE:0000667 ! TMT10PLEX is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000522 name: TMT128N def: "TMT128N" [PRIDE:PRIDE] is_a: PRIDE:0000667 ! TMT10PLEX is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000523 name: TMT129 def: "TMT129" [PRIDE:PRIDE] is_a: PRIDE:0000666 ! TMT6PLEX [Term] id: PRIDE:0000524 name: TMT129C def: "TMT129C" [PRIDE:PRIDE] is_a: PRIDE:0000667 ! TMT10PLEX is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000525 name: TMT129N def: "TMT129N" [PRIDE:PRIDE] is_a: PRIDE:0000667 ! TMT10PLEX is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000526 name: TMT130 def: "TMT130" [PRIDE:PRIDE] is_a: PRIDE:0000666 ! TMT6PLEX [Term] id: PRIDE:0000527 name: TMT130C def: "TMT130C" [PRIDE:PRIDE] is_a: PRIDE:0000667 ! TMT10PLEX is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000528 name: TMT130N def: "TMT130N" [PRIDE:PRIDE] is_a: PRIDE:0000667 ! TMT10PLEX is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000529 name: TMT131 def: "TMT131" [PRIDE:PRIDE] is_a: PRIDE:0000666 ! TMT6PLEX is_a: PRIDE:0000667 ! TMT10PLEX [Term] id: PRIDE:0000530 name: ITRAQ def: "ITRAQ channel label" [PRIDE:PRIDE] is_a: PRIDE:0000514 ! Quantification channel label [Term] id: PRIDE:0000531 name: ITRAQ113 def: "ITRAQ113 channel" [PRIDE:PRIDE] is_a: PRIDE:0000530 ! ITRAQ [Term] id: PRIDE:0000532 name: ITRAQ114 def: "ITRAQ114 channel" [PRIDE:PRIDE] is_a: PRIDE:0000530 ! ITRAQ [Term] id: PRIDE:0000533 name: ITRAQ115 def: "ITRAQ115 channel" [PRIDE:PRIDE] is_a: PRIDE:0000530 ! ITRAQ [Term] id: PRIDE:0000534 name: ITRAQ116 def: "ITRAQ116 channel" [PRIDE:PRIDE] is_a: PRIDE:0000530 ! ITRAQ [Term] id: PRIDE:0000535 name: ITRAQ117 def: "ITRAQ117 channel" [PRIDE:PRIDE] is_a: PRIDE:0000530 ! ITRAQ [Term] id: PRIDE:0000536 name: ITRAQ118 def: "ITRAQ118 channel" [PRIDE:PRIDE] is_a: PRIDE:0000530 ! ITRAQ [Term] id: PRIDE:0000537 name: ITRAQ119 def: "ITRAQ119 channel" [PRIDE:PRIDE] is_a: PRIDE:0000530 ! ITRAQ [Term] id: PRIDE:0000538 name: ITRAQ121 def: "ITRAQ121 channel" [PRIDE:PRIDE] is_a: PRIDE:0000530 ! ITRAQ [Term] id: PRIDE:0000541 name: ICAT heavy def: "ICAT heavy" [PRIDE:PRIDE] is_a: PRIDE:0000319 ! ICAT channel label [Term] id: PRIDE:0000542 name: ICAT light def: "ICAT light" [PRIDE:PRIDE] is_a: PRIDE:0000319 ! ICAT channel label [Term] id: PRIDE:0000543 name: Quality Control def: "MS experiments conducted to control the quality of measurements" [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000544 name: Quality Control Sample def: "Sample with known content and quantities designed to control the consistent quality of measurement for a particular method and settings" [PRIDE:PRIDE] is_a: PRIDE:0000017 ! Sample description additional parameter [Term] id: PRIDE:0000545 name: QC1 sample def: "QC1 sample as described in 10.1371/journal.pone.0189209" [PRIDE:PRIDE] is_a: PRIDE:0000544 ! Quality Control Sample [Term] id: PRIDE:0000546 name: QC2 sample def: "QC2 sample as described in 10.1371/journal.pone.0189209" [PRIDE:PRIDE] is_a: PRIDE:0000544 ! Quality Control Sample [Term] id: PRIDE:0000547 name: Instrument properties def: "Instrument properties" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: MS:1000451 name: mass analyzer def: "Mass analyzer" [PRIDE:PRIDE] is_a: PRIDE:0000547 ! Instrument properties [Term] id: PRIDE:0000548 name: MS1 mass analyzer def: "MS1 mass analyzer" [PRIDE:PRIDE] is_a: MS:1000451 ! mass analyzer [Term] id: PRIDE:0000549 name: MS2 mass analyzer def: "MS2 mass analyzer" [PRIDE:PRIDE] is_a: MS:1000451 ! mass analyzer [Term] id: PRIDE:0000550 name: Fractionation method def: "Umbrella term for different types of fractionation methods" [PRIDE:PRIDE] is_a: PRIDE:0000021 ! Fractionation [Term] id: PRIDE:0000551 name: Separation method def: "Umbrella term for different types of separation methods" [PRIDE:PRIDE] is_a: PRIDE:0000022 ! Separation [Term] id: PRIDE:0000552 name: Off-gel electrophoresis def: "Fractionate peptides into discrete liquid fractions based on isoelectric electrophoresis (10.1002/elps.200390030)" [PRIDE:PRIDE] is_a: PRIDE:0000550 ! Fractionation method [Term] id: PRIDE:0000553 name: Isoelectric focusing def: "An electrophoresis method for the separation of amphoteric analytes according to their isoelectric points by the application of an electric field along a pH gradient" [PRIDE:PRIDE] is_a: PRIDE:0000550 ! Fractionation method [Term] id: PRIDE:0000554 name: Hydrophilic interaction chromatography (HILIC) def: "Liquid chromatography where the stationary phase is hydrophilic, the mobile phase is organic and separation is achieved based on polarity" [PRIDE:PRIDE] is_a: PRIDE:0000562 ! Normal-phase liquid chromatography (NP) [Term] id: PRIDE:0000555 name: ERLIC def: "Electrostatic repulsion hydrophilic interaction chromatography (ERLIC). Hydrophilic interaction chromatography where the chromatography column is an ion-exchange column and the mobile phase is predominantly organic" [PRIDE:PRIDE] is_a: PRIDE:0000562 ! Normal-phase liquid chromatography (NP) [Term] id: PRIDE:0000556 name: Ion-exchange chromatography def: "A chromatography method where the separation is caused by differences in ion-exchange affinity" [PRIDE:PRIDE] is_a: PRIDE:0000565 ! High-performance liquid chromatography [Term] id: PRIDE:0000557 name: Size-exclusion chromatography (SEC) def: "A chromatography method where the separation is caused by differences in molecular size" [PRIDE:PRIDE] is_a: PRIDE:0000565 ! High-performance liquid chromatography [Term] id: PRIDE:0000558 name: Strong anion-exchange chromatography (SAX) def: "A chromatography method with the stationary phase being a strong anion exchanger" [PRIDE:PRIDE] is_a: PRIDE:0000556 ! Ion-exchange chromatography [Term] id: PRIDE:0000559 name: Weak anion-exchange chromatography (WAX) def: "A chromatography method with the stationary phase being a weak anion exchanger" [PRIDE:PRIDE] is_a: PRIDE:0000556 ! Ion-exchange chromatography [Term] id: PRIDE:0000560 name: Weak cation-exchange chromatography (WCX) def: "A chromatography method with the stationary phase being a weak cation exchanger" [PRIDE:PRIDE] is_a: PRIDE:0000556 ! Ion-exchange chromatography [Term] id: PRIDE:0000561 name: Strong cation-exchange chromatography (SCX) def: "A chromatography method with the stationary phase being a strong cation exchanger" [PRIDE:PRIDE] is_a: PRIDE:0000556 ! Ion-exchange chromatography [Term] id: PRIDE:0000562 name: Normal-phase liquid chromatography (NP) def: "Liquid chromatography where the stationary phase is more polar than the mobile phase. This is the default for liquid chromatography" [PRIDE:PRIDE] is_a: PRIDE:0000565 ! High-performance liquid chromatography [Term] id: PRIDE:0000563 name: Reversed-phase chromatography (RP) def: "Liquid chromatography where the mobile phase is significantly more polar than the stationary phase" [PRIDE:PRIDE] is_a: PRIDE:0000565 ! High-performance liquid chromatography [Term] id: PRIDE:0000564 name: High-pH reversed-phase chromatography (hpHRP) def: "Liquid chromatography where the mobile phase is of high pH and significantly more polar than the stationary phase" [PRIDE:PRIDE] is_a: PRIDE:0000563 ! Reversed-phase chromatography (RP) [Term] id: PRIDE:0000565 name: High-performance liquid chromatography def: "Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high" [PRIDE:PRIDE] xref: http://purl.obolibrary.org/obo/CHMO_0001009 is_a: PRIDE:0000550 ! Fractionation method is_a: PRIDE:0000551 ! Separation method [Term] id: PRIDE:0000566 name: High-resolution isoelectric focusing (HiRIEF) def: "An electrophoresis method with significantly higher resolution than common isoelectric focusing methods" [PRIDE:PRIDE] is_a: PRIDE:0000553 ! Isoelectric focusing [Term] id: PRIDE:0000567 name: Gel electrophoresis def: "Gel electrophoresis" [PRIDE:PRIDE] is_a: PRIDE:0000550 ! Fractionation method [PRIDE:PRIDE] is_a: PRIDE:0000551 ! Separation method [Term] id: PRIDE:0000568 name: SDS PAGE def: "SDS-PAGE is an electrophoresis method that allows protein separation by mass. The medium/matrix is a polyacrylamide-based discontinuous gel" [PRIDE:PRIDE] is_a: PRIDE:0000567 ! Gel electrophoresis [Term] id: PRIDE:0000569 name: 2D PAGE def: "2D-PAGE is a form of gel electrophoresis in which separation and identification of proteins in a sample are done by displacement in 2 dimensions oriented at right angles to one another(orthogonal)" [PRIDE:PRIDE] is_a: PRIDE:0000567 ! Gel electrophoresis [Term] id: PRIDE:0000571 name: Quantification software def: "A software that perform protein quantification using mass spectrometry data" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000572 name: OpenMS def: "OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software" [PRIDE:PRIDE] is_a: PRIDE:0000571 ! Quantification software is_a: PRIDE:0000573 ! Identification software [Term] id: PRIDE:0000573 name: Identification software def: "A software that perform peptide/protein identification using mass spectrometry data" [PRIDE:PRIDE] is_a: BFO:0000001 ! entity [Term] id: PRIDE:0000574 name: MaxQuant def: "MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data" [PRIDE:PRIDE] is_a: PRIDE:0000571 ! Quantification software is_a: PRIDE:0000573 ! Identification software [Term] id: PRIDE:0000575 name: precursor mass tolerance def: "Threshold at precursor level to compare experimental mass with theoretical mass" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000576 name: fragment mass tolerance def: "Threshold at fragment level to compare experimental mass with theoretical mass" [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter [Term] id: PRIDE:0000577 name: file uri def: "URI of one external file associated to the PRIDE experiment on SDRF files definitions" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000578 name: Bound fraction def: "The bound fraction after a depletion process" [PRIDE:PRIDE] is_a: PRIDE:0000020 ! Depletion [Term] id: PRIDE:0000579 name: Depleted fraction def: "The depleted fraction after a depletion process" [PRIDE:PRIDE] is_a: PRIDE:0000020 ! Depletion [Term] id: MS:1002038 name: label free sample def: "A sample that has not been labelled or modified" [PRIDE:PRIDE] is_a: PRIDE:0000514 ! Quantification channel label [Term] id: PRIDE:0000580 name: TMT131N def: "TMT131N" [PRIDE:PRIDE] is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000581 name: TMT131C def: "TMT131C" [PRIDE:PRIDE] is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000582 name: TMT132N def: "TMT132N" [PRIDE:PRIDE] is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000583 name: TMT132C def: "TMT132C" [PRIDE:PRIDE] is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000584 name: Experimental design file URI def: "Experimental design file URI" [PRIDE:PRIDE] is_a: PRIDE:0000403 ! Associated file URI is_a: PRIDE:0000577 ! file uri [Term] id: PRIDE:0000585 name: Enrichment def: "Enrichment of specific post-translational modifications" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000586 name: Enrichment method def: "Enrichment method Enrichment of specific post-translational modifications" [PRIDE:PRIDE] is_a: PRIDE:0000585 ! Enrichment [Term] id: PRIDE:0000587 name: IMAC def: "The combination of immobilized metal affinity chromatography (IMAC) and mass spectrometry is a widely used technique for enrichment and sequencing of phosphopeptides" [PRIDE:PRIDE] is_a: PRIDE:0000586 ! Enrichment method [Term] id: PRIDE:0000588 name: TIO2 def: "Titanium dioxide (TiO2) has very high affinity for phosphopeptides and in recent years it has become one of the most popular methods for phosphopeptide enrichment from complex biological samples" [PRIDE:PRIDE] is_a: PRIDE:0000586 ! Enrichment method [Term] id: MS:1000044 name: dissociation method def: "Fragmentation method used for dissociation or fragmentation" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000589 name: EThcD def: "A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy)" [PRIDE:PRIDE] is_a: MS:1000044 ! dissociation method is_a: PRIDE:0000644 ! MS2 dissociation method is_a: PRIDE:0000645 ! MS3 dissociation method [Term] id: PRIDE:0000590 name: HCD def: "Beam-type collision-induced dissociation" [PRIDE:PRIDE] is_a: MS:1000044 ! dissociation method is_a: PRIDE:0000644 ! MS2 dissociation method is_a: PRIDE:0000645 ! MS3 dissociation method [Term] id: PRIDE:0000591 name: CID def: "Collision-induced dissociation" [PRIDE:PRIDE] is_a: MS:1000044 ! dissociation method is_a: PRIDE:0000644 ! MS2 dissociation method is_a: PRIDE:0000645 ! MS3 dissociation method [Term] id: PRIDE:0000592 name: ETciD def: "ETD with supplemental activation" [PRIDE:PRIDE] synonym: "ETcaD" EXACT [PRIDE] is_a: MS:1000044 ! dissociation method is_a: PRIDE:0000644 ! MS2 dissociation method is_a: PRIDE:0000645 ! MS3 dissociation method [Term] id: MS:1000045 name: collision energy def: "Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion" [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter [Term] id: PRIDE:0000593 name: CID collision energy def: "CID collision energy" [PRIDE:PRIDE] is_a: MS:1000045 ! collision energy is_a: PRIDE:0000591 ! CID [Term] id: PRIDE:0000594 name: HCD collision energy def: "HCD collision energy" [PRIDE:PRIDE] is_a: MS:1000045 ! collision energy is_a: PRIDE:0000590 ! HCD [Term] id: PRIDE:0000595 name: EThcD collision energy def: "EThcD collision energy" [PRIDE:PRIDE] is_a: MS:1000045 ! collision energy is_a: PRIDE:0000589 ! EThcD [Term] id: PRIDE:0000596 name: ETciD collision energy def: "ETciD collision energy" [PRIDE:PRIDE] is_a: MS:1000045 ! collision energy is_a: PRIDE:0000592 ! ETciD [Term] id: PRIDE:0000597 name: metabolic label def: "Metabolic label" [PRIDE:PRIDE] is_a: PRIDE:0000514 ! Quantification channel label [Term] id: PRIDE:0000598 name: Alkylation reagent def: "The alkylation reagent that is used to covalently modify cysteine SH-groups after reduction, preventing them from forming unwanted novel disulfide bonds" [PRIDE:PRIDE] is_a: PRIDE:0000026 ! Alkylation [Term] id: PRIDE:0000599 name: Iodoacetamide (IAA) def: "The alkylation reagent 2-iodoacetamide with the chemical formula - C2H4INO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da" [PRIDE:PRIDE] is_a: PRIDE:0000598 ! Alkylation reagent [Term] id: PRIDE:0000600 name: Chloroacetamide (ClAA) def: "The alkylation reagent 2-chloroacetamide with the chemical formula - C2H4ClNO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da" [PRIDE:PRIDE] is_a: PRIDE:0000598 ! Alkylation reagent [Term] id: PRIDE:0000601 name: Iodoacetic acid (IAC) def: "The derivative of acetic acid with the chemical formula - C2H3IO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da" [PRIDE:PRIDE] is_a: PRIDE:0000598 ! Alkylation reagent [Term] id: PRIDE:0000602 name: Chloroacetic acid (ClAC) def: "The derivative of acetic acid with the chemical formula - C2H3ClO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da" [PRIDE:PRIDE] is_a: PRIDE:0000598 ! Alkylation reagent [Term] id: PRIDE:0000603 name: Acrylamide (AA) def: "The alkylation reagent acrylamide (or acrylic amide) with the chemical formula - C3H5NO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 24) - 71.037 Da" [PRIDE:PRIDE] is_a: PRIDE:0000598 ! Alkylation reagent [Term] id: PRIDE:0000604 name: 4-Vinylpyridine (4-VP) def: "The derivative of pyridine with a vinyl group in the 4-position with the chemical formula - C7H7N. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 31) - 105.058 Da" [PRIDE:PRIDE] is_a: PRIDE:0000598 ! Alkylation reagent [Term] id: PRIDE:0000605 name: Methyl methanethiosulfonate (MMTS) def: "The alkylation reagent that can reversibly sulfenylate thiol-containing molecules, chemical formula - C2H6O2S2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 39) - 45.988 Da" [PRIDE:PRIDE] is_a: PRIDE:0000598 ! Alkylation reagent [Term] id: PRIDE:0000606 name: N-ethylmaleimide (NEM) def: "The derivative of maleic acid, chemical formula - C6H7NO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 108) - 125.048 Da" [PRIDE:PRIDE] is_a: PRIDE:0000598 ! Alkylation reagent [Term] id: PRIDE:0000607 name: Reduction reagent def: "The chemical reagent that is used to break disulfide bonds in proteins" [PRIDE:PRIDE] is_a: PRIDE:0000025 ! Reduction [Term] id: PRIDE:0000608 name: Dithiothreitol (DTT) def: "The commonly used small redox reagent dithiothreitol (also known as Cleland's reagent) with chemical formula C4H10O2S2" [PRIDE:PRIDE] is_a: PRIDE:0000607 ! Reduction reagent [Term] id: PRIDE:0000609 name: Tris(2-carboxyethyl)phosphine (TCEP) def: "The reduction agent with chemincal formuls C9H15O6P" [PRIDE:PRIDE] is_a: PRIDE:0000607 ! Reduction reagent [Term] id: PRIDE:0000610 name: Beta-mercaptoethanol (BME) def: "The reduction agent 2-mercaptoethanol (2-sulfanylethan-1-ol) with chemincal formuls C2H6OS" [PRIDE:PRIDE] is_a: PRIDE:0000607 ! Reduction reagent [Term] id: PRIDE:0000611 name: SILAC light R:12C(6)14N(4) def: "The light amino acid arginine used in SILAC experiments, using the following isotopes:12C(6)14N(4)" [PRIDE:PRIDE] is_a: PRIDE:0000326 ! SILAC light [Term] id: PRIDE:0000612 name: SILAC light L:12C(6) def: "The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6)" [PRIDE:PRIDE] is_a: PRIDE:0000326 ! SILAC light [Term] id: PRIDE:0000613 name: SILAC light K:12C(6)14N(2) def: "The light amino acid lysine used in SILAC experiments, using the following isotopes:12C(6)14N(2)" [PRIDE:PRIDE] is_a: PRIDE:0000326 ! SILAC light [Term] id: PRIDE:0000614 name: SILAC light P:12C(5) def: "The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5)" [PRIDE:PRIDE] is_a: PRIDE:0000326 ! SILAC light [Term] id: PRIDE:0000615 name: SILAC heavy R:13C(6)15N(4) def: "The heavy amino acid arginine used in SILAC experiments, using the following isotopes:13C(6)15N(4)" [PRIDE:PRIDE] is_a: PRIDE:0000325 ! SILAC heavy [Term] id: PRIDE:0000616 name: SILAC heavy L:13C(6) def: "The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6)" [PRIDE:PRIDE] is_a: PRIDE:0000325 ! SILAC heavy [Term] id: PRIDE:0000617 name: SILAC heavy K:13C(6)15N(2) def: "The heavy amino acid lysine used in SILAC experiments, using the following isotopes:13C(6)15N(2)" [PRIDE:PRIDE] is_a: PRIDE:0000325 ! SILAC heavy [Term] id: PRIDE:0000618 name: SILAC medium R:13C(6)14N(4) def: "The medium amino acid arginine used in SILAC experiments, using the following isotopes: 13C(6)14N(4)" [PRIDE:PRIDE] is_a: PRIDE:0000327 ! SILAC medium [Term] id: PRIDE:0000619 name: SILAC medium K:13C(6)14N(2) def: "The medium amino acid lysine used in SILAC experiments, using the following isotopes: 13C(6)14N(2)" [PRIDE:PRIDE] is_a: PRIDE:0000327 ! SILAC medium [Term] id: PRIDE:0000620 name: 15N def: "Metabolic label 15N" [PRIDE:PRIDE] is_a: PRIDE:0000597 ! metabolic label [Term] id: PRIDE:0000621 name: 13C def: "Metabolic label 13C" [PRIDE:PRIDE] is_a: PRIDE:0000597 ! metabolic label [Term] id: PRIDE:0000623 name: original source name def: "Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics" [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000624 name: SpectraCluster MaxRatio def: "Spectra Cluster Maximum Ratio for the cluster" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000625 name: NIST ProbCorr def: "NIST Probability Correlation" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000626 name: NIST Dotbest def: "NIST best dot product" [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter [Term] id: PRIDE:0000627 name: Data-dependent acquisition def: "Data-dependent acquisition" [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics is_a: PRIDE:0000659 ! Proteomics data acquisition method [Term] id: PRIDE:0000629 name: Parallel reaction monitoring def: "Parallel Reaction Monitoring (PRM)" [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics is_a: PRIDE:0000659 ! Proteomics data acquisition method [Term] id: PRIDE:0000630 name: Selected reaction monitoring def: "Selected reaction monitoring (SRM)" [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics is_a: PRIDE:0000659 ! Proteomics data acquisition method [Term] id: PRIDE:0000631 name: Mass spectrometry imaging def: "Mass spectrometry imaging" [PRIDE:PRIDE] is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy [Term] id: PRIDE:0000632 name: TMT133N def: "TMT133N" [PRIDE:PRIDE] is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000633 name: TMT133C def: "TMT133C" [PRIDE:PRIDE] is_a: PRIDE:0000668 ! TMT16PLEX is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000634 name: TMT134 def: "TMT134" [PRIDE:PRIDE] is_a: PRIDE:0000668 ! TMT16PLEX [Term] id: PRIDE:0000635 name: Affinity proteomics def: "The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes" [PRIDE:PRIDE] is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000636 name: SomaScan affinity proteomics def: "Refer to technologies like SomaScan that employ aptamers as the binding agents for protein detection. SomaScan utilizes Slow Off-rate Modified Aptamers (SOMAmers) for protein targeting and measurement" [PRIDE:PRIDE] is_a: PRIDE:0000635 ! Affinity proteomics [Term] id: PRIDE:0000637 name: Olink affinity proteomics def: "Refer to technologies like Olink that utilize antibodies as the primary binding agents for protein detection. Olink's Proximity Extension Assay (PEA) technology relies on using antibody pairs to generate protein-specific signals" [PRIDE:PRIDE] is_a: PRIDE:0000635 ! Affinity proteomics [Term] id: PRIDE:0000638 name: Instrument model def: "Instrument model" [PRIDE:PRIDE] is_a: PRIDE:0000547 ! Instrument properties [Term] id: PRIDE:0000639 name: Somalogic instrument model def: "Somalogic instrument model" [PRIDE:PRIDE] is_a: PRIDE:0000638 ! Instrument model [Term] id: PRIDE:0000640 name: SomaScan assay v4.0 def: "SomaScan assay v4.0" [PRIDE:PRIDE] is_a: PRIDE:0000639 ! Somalogic instrument model [Term] id: PRIDE:0000641 name: SomaScan assay v4.1 def: "SomaScan assay v4.1" [PRIDE:PRIDE] is_a: PRIDE:0000639 ! Somalogic instrument model [Term] id: PRIDE:0000642 name: TMT134C def: "TMT134C" [PRIDE:PRIDE] is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000643 name: TMT134N def: "TMT134N" [PRIDE:PRIDE] is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000644 name: MS2 dissociation method def: "Fragmentation method used for dissociation or fragmentation for MS2" [PRIDE:PRIDE] is_a: MS:1000044 ! dissociation method [Term] id: PRIDE:0000645 name: MS3 dissociation method def: "Fragmentation method used for dissociation or fragmentation for MS3" [PRIDE:PRIDE] is_a: MS:1000044 ! dissociation method [Term] id: PRIDE:0000646 name: MS3 mass analyzer def: "MS3 mass analyzer" [PRIDE:PRIDE] is_a: MS:1000451 ! mass analyzer [Term] id: PRIDE:0000649 name: Immunopeptidomics def: "Immunopeptidomics is a large-scale method capable of identifying and quantifying the presented HLA immunopeptidome" [PRIDE:PRIDE] is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy is_a: PRIDE:0000457 ! Experiment Type [Term] id: PRIDE:0000650 name: diaPASEF def: "Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825" [PRIDE:PRIDE] is_a: PRIDE:0000450 ! Data-independent acquisition [Term] id: PRIDE:0000651 name: Absolute quantification def: "Absolute quantification precisely measures the concentration of a specific analyte in a sample" [PRIDE:PRIDE] is_a: PRIDE:0000307 ! Quantification method [Term] id: PRIDE:0000652 name: Relative quantification def: "Relative quantification compares the concentrations of analytes (e.g., a proteins) across different samples" [PRIDE:PRIDE] is_a: PRIDE:0000307 ! Quantification method [Term] id: PRIDE:0000653 name: NPX def: "Normalized Protein eXpression" [PRIDE:PRIDE] is_a: PRIDE:0000652 ! Relative quantification [Term] id: PRIDE:0000654 name: Olink instrument model def: "Olink instrument model" [PRIDE:PRIDE] is_a: PRIDE:0000638 ! Instrument model [Term] id: PRIDE:0000655 name: Olink Target 96 def: "Olink Target 96 is a proteomics platform offering targeted analysis of 92 specific protein biomarkers per panel using proximity extension assay (PEA) technology" [PRIDE:PRIDE] is_a: PRIDE:0000672 ! Olink Target [Term] id: PRIDE:0000656 name: Olink Explore 1536 def: "Olink Explore 1536" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Olink Explore [Term] id: PRIDE:0000657 name: Olink Explore 3072/384 def: "Olink Explore 3072 includes eight 384-plex panels for efficient, large-scale, disease- and process-focused studies" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Olink Explore [Term] id: PRIDE:0000658 name: Olink Explore 384 def: "Olink Explore 384" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Olink Explore [Term] id: PRIDE:0000659 name: Proteomics data acquisition method def: "Proteomics data acquisition method" [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics [Term] id: PRIDE:0000660 name: Ion Mobility Separation def: "Ion Mobility Separation" [PRIDE:PRIDE] is_a: PRIDE:0000551 ! Separation method [Term] id: PRIDE:0000661 name: Differential mobility Separation def: "Differential mobility Separation" [PRIDE:PRIDE] is_a: PRIDE:0000551 ! Separation method [Term] id: PRIDE:0000662 name: SelexION Separation Method def: "SelexION differential mobility separation device" [PRIDE:PRIDE] is_a: PRIDE:0000660 ! Ion Mobility Spectrometry is_a: PRIDE:0000661 ! Differential mobility spectrometry [Term] id: PRIDE:0000663 name: technology type def: "The technology type or platform used to perform the study" [EFO:EFO_0005521] is_a: PRIDE:0000006 ! Experiment additional parameter [Term] id: PRIDE:0000664 name: proteomic profiling by mass spectrometry def: "An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry" [EFO:EFO_0002766] is_a: PRIDE:0000663 ! technology type [Term] id: PRIDE:0000665 name: Glycoproteomics def: "Study of proteins that identifies, catalogs, and characterizes those proteins that contain carbohydrates as posttranslational modifications" [PRIDE:PRIDE] is_a: PRIDE:0000457! Experiment Type [Term] id: PRIDE:0000666 name: TMT6PLEX def: "TMT 6-plex labeling kit has 6 channels" [PRIDE:PRIDE] is_a: PRIDE:0000314 ! TMT [Term] id: PRIDE:0000667 name: TMT10PLEX def: "TMT 10-plex labeling kit has 10 channels" [PRIDE:PRIDE] is_a: PRIDE:0000314 ! TMT [Term] id: PRIDE:0000668 name: TMT16PLEX def: "TMT 16-plex labeling kit has 16 channels" [PRIDE:PRIDE] is_a: PRIDE:0000314 ! TMT [Term] id: PRIDE:0000669 name: TMT18PLEX def: "TMT 18-plex labeling kit has 18 channels" [PRIDE:PRIDE] is_a: PRIDE:0000314 ! TMT [Term] id: PRIDE:0000670 name: TMT135 def: "TMT135" [PRIDE:PRIDE] is_a: PRIDE:0000669 ! TMT18PLEX [Term] id: PRIDE:0000671 name: Olink Explore def: "Olink Explore is a high-throughput proteomics platform that quantifies protein biomarkers across multiple samples using proximity extension assay (PEA) technology" [PRIDE:PRIDE] is_a: PRIDE:0000654 ! Olink instrument model [Term] id: PRIDE:0000672 name: Olink Target def: "Olink Target is a proteomics platform designed for focused, customizable analysis of specific protein biomarker panels using proximity extension assay (PEA) technology" [PRIDE:PRIDE] is_a: PRIDE:0000654 ! Olink instrument model [Term] id: PRIDE:0000673 name: Olink Explore HT def: "The Olink Explore HT is a high-throughput proteomics platform for large-scale biomarker discovery, enabling simultaneous measurement of thousands of proteins from minimal sample volumes" [PRIDE:PRIDE] is_a: PRIDE:0000671 ! Olink Explore [Term] id: PRIDE:0000674 name: human gut def: "A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their gut-associated microbiome." [PRIDE:PRIDE] is_a: UBERON:0005409 ! gastrointestinal system [Term] id: PRIDE:0000675 name: sample name def: "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. MIXS:0001107" [PRIDE:PRIDE] synonym: "sample name" EXACT [] is_a: NCIT:C25507 ! Data Field relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000676 name: project name def: "Name of the project within which the sequencing was organized. MIXS:0000092" [PRIDE:PRIDE] synonym: "project name" EXACT [] is_a: NCIT:C25507 ! Data Field relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000677 name: gastrointestinal tract disorder def: "History of gastrointestinal tract disorders; can include multiple disorders. MIXS:0000280" [PRIDE:PRIDE] is_a: MONDO:0000001 ! Disease relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000678 name: liver disorder def: "History of liver disorders; can include multiple disorders. MIXS:0000282" [PRIDE:PRIDE] is_a: MONDO:0000001 ! Disease relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000679 name: special diet def: "Specification of special diet; can include multiple special diets. MIXS:0000905" [PRIDE:PRIDE] is_a: EFO:0002755 ! Diet relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000680 name: host subject id def: "A unique identifier by which each subject can be referred to, de-identified. MIXS:0000861" [PRIDE:PRIDE] is_a: NCIT:C25507 ! Data Field relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000681 name: host age def: "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees. MIXS:0000255" [PRIDE:PRIDE] synonym: "host age slot" EXACT [] is_a: NCIT:C25507 ! Data Field relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000682 name: host disease status def: "List of diseases with which the host has been diagnosed; can include multiple diagnoses. MIXS:0000031" [PRIDE:PRIDE] synonym: "host disease slot" EXACT [] is_a: NCIT:C25507 ! Data Field relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000683 name: IHMC medication code def: "Can include multiple medication codes. MIXS:0000884" [PRIDE:PRIDE] is_a: NCIT:C25162 ! Code relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000684 name: chemical administration def: "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. MIXS:0000751" [PRIDE:PRIDE] is_a: PECO:0007086 ! chemical fertilizer exposure relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000685 name: host body site def: "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc.). MIXS:0000867" [PRIDE:PRIDE] is_a: NCIT:C12219 ! Anatomic Structure, System, or Substance relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000686 name: host body product def: "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. MIXS:0000888" [PRIDE:PRIDE] is_a: NCIT:C12219 ! Anatomic Structure, System, or Substance relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000687 name: host total mass def: "Total mass of the host at collection, the unit depends on host. MIXS:0000263" [PRIDE:PRIDE] is_a: OBA:2045413 ! anatomical entity mass relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000688 name: host height def: "The height of subject. MIXS:0000264" [PRIDE:PRIDE] synonym: "body height" EXACT [] is_a: NCIT:C25347 ! Height relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000689 name: host diet def: "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types. MIXS:0000869" [PRIDE:PRIDE] is_a: EFO:0002755 ! Diet relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000690 name: host last meal def: "Content of last meal and time since feeding; can include multiple values. MIXS:0000870" [PRIDE:PRIDE] is_a: NCIT:C80248 ! Meal relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000691 name: host family relationship def: "Relationships to other hosts in the same study; can include multiple relationships. MIXS:0000872" [PRIDE:PRIDE] synonym: "family relationship" EXACT [] is_a: BFO:0000016 ! disposition relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000692 name: host genotype def: "Observed genotype MIXS:0000365" [PRIDE:PRIDE] is_a: EFO:0004554 ! genomic measurement relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000693 name: host phenotype def: "Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP). MIXS:0000274" [PRIDE:PRIDE] is_a: BFO:0000019 ! quality relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000694 name: host body temperature def: "Core body temperature of the host when sample was collected. MIXS:0000874" [PRIDE:PRIDE] is_a: NCIT:C25206 ! Temperature relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000695 name: host body-mass index def: "Body mass index, calculated as weight/(height)squared. MIXS:0000317" [PRIDE:PRIDE] is_a: EFO:0004324 ! body weights and measurements relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000696 name: ethnicity def: "A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. MIXS:0000895" [PRIDE:PRIDE] is_a: BFO:0000019 ! quality relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000697 name: host occupation def: "Most frequent job performed by subject. MIXS:0000896" [PRIDE:PRIDE] is_a: NCIT:C19160 ! Occupation or Discipline relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000698 name: medical history performed def: "Whether full medical history was collected. MIXS:0000897" [PRIDE:PRIDE] is_a: NCIT:C16205 ! Healthcare activity relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000699 name: host pulse def: "Resting pulse, measured as beats per minutes. MIXS:0000333" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000700 name: perturbation def: "Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types. MIXS:0000754" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000701 name: salinity def: "The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater. MIXS:0000183" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000702 name: oxygenation status of sample def: "Oxygenation status of the sample. MIXS:0000753" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000703 name: temperature def: "Temperature of the sample at the time of sampling. MIXS:0000113" [PRIDE:PRIDE] is_a: NCIT:C25447! Characteristic relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000704 name: organism count def: "Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr). MIXS:0000103" [PRIDE:PRIDE] is_a: MMO:0000222 ! isolated cell method relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000705 name: sample storage temperature def: "Temperature at which sample was stored, e.g. -80 degree Celsius. MIXS:0000110" [PRIDE:PRIDE] is_a: NCIT:C45279 ! Log relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000706 name: sample volume or weight for DNA extraction def: "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001). MIXS:0000111" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000707 name: sample storage duration def: "Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format. MIXS:0000116" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000708 name: observed host symbionts def: "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont can have its own symbionts. For example, parasites may have hyperparasites (=parasites of the parasite). MIXS:0001298" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000709 name: sample storage location def: "Location at which sample was stored, usually name of a specific freezer/room. MIXS:0000755" [PRIDE:PRIDE] is_a: GENEPIO:0100586 ! data field relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut [Term] id: PRIDE:0000710 name: miscellaneous parameter def: "Any other measurement performed or parameter collected, that is not listed here. MIXS:0000752" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000674 ! Human gut relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000711 name: depth def: "The vertical distance below local surface. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples MIXS:0000018" [PRIDE:PRIDE] is_a: NCIT:C25447 ! Characteristic relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000712 name: elevation def: "Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit MIXS:0000093" [PRIDE:PRIDE] is_a: PATO:0000140 ! Position relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000713 name: current land use def: "Present state of sample site MIXS:0001080" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000714 name: current vegetation def: "Vegetation classification from one or more standard classification systems, or agricultural crop MIXS:0000312" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000715 name: current vegetation method def: "Reference or method used in vegetation classification MIXS:0000314" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000716 name: history of previous land use def: "Previous land use and dates MIXS:0000315" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000717 name: history of previous land use method def: "Reference or method used in determining previous land use and dates MIXS:0000316" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000718 name: history of crop rotation def: "Whether or not crop is rotated, and if yes, rotation schedule MIXS:0000318" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000719 name: history of agrochemical additions def: "Addition of fertilizers, pesticides, etc. - amount and time of applications MIXS:0000639" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000720 name: history of tillage def: "Note method(s) used for tilling MIXS:0001081" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000721 name: history of fire def: "Historical and/or physical evidence of fire MIXS:0001086" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000722 name: history of flooding def: "Historical and/or physical evidence of flooding MIXS:0000319" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000723 name: history of extreme event def: "Unusual physical events that may have affected microbial populations MIXS:0000320" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000724 name: soil horizon def: "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath MIXS:0001082" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000725 name: horizon method def: "Reference or method used in determining the horizon MIXS:0000321" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000726 name: sieving def: "Collection design of pooled samples and/or sieve size and amount of sample sieved MIXS:0000322" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000727 name: water content def: "Water content measurement MIXS:0000185" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000728 name: water content method def: "Reference or method used in determining the water content of soil MIXS:0000323" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000729 name: pooling of DNA extracts def: "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given MIXS:0000325" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000730 name: storage conditions def: "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other) MIXS:0000327" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000731 name: link to climate information def: "Link to climate resource MIXS:0000328" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000732 name: mean annual temperature def: "Mean annual temperature MIXS:0000642" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000733 name: mean seasonal temperature def: "Mean seasonal temperature MIXS:0000643" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000734 name: mean annual precipitation def: "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps MIXS:0000644" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000735 name: mean seasonal precipitation def: "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps MIXS:0000645" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000736 name: link to classification information def: "Link to digitized soil maps or other soil classification information MIXS:0000329" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000737 name: soil taxonomic of FAO classification def: "Soil classification from the FAO World soil distribution from International Soil Reference and Information Centre (ISRIC). The list of available soil classifications can be found at https://www.isric.org/explore/world-soil-distribution MIXS:0001083" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000738 name: soil taxonomic of local classification def: "Soil classification based on local soil classification system MIXS:0000330" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000739 name: soil taxonomic of local classification method def: "Reference or method used in determining the local soil classification MIXS:0000331" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000740 name: slope gradient def: "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer MIXS:0000646" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000741 name: slope aspect def: "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration MIXS:0000647" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000742 name: profile position def: "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas MIXS:0001084" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000743 name: drainage classification def: "Drainage classification from a standard system such as the USDA system MIXS:0001085" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000744 name: soil texture def: "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional MIXS:0000335" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000745 name: soil texture method def: "Reference or method used in determining soil texture MIXS:0000336" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000746 name: pH def: "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid MIXS:0001001" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000747 name: pH method def: "Reference or method used in determining pH MIXS:0001106" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000748 name: organic matter def: "Concentration of organic matter MIXS:0000204" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000749 name: total organic carbon def: "Total organic carbon content MIXS:0000533" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000750 name: total organic carbon method def: "Reference or method used in determining total organic carbon MIXS:0000337" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000751 name: total nitrogen content def: "Total nitrogen content of the sample MIXS:0000530" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000752 name: total nitrogen content method def: "Reference or method used in determining the total nitrogen MIXS:0000338" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000753 name: microbial biomass def: "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units MIXS:0000650" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000754 name: microbial biomass method def: "Reference or method used in determining microbial biomass MIXS:0000339" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000755 name: links to additional analysis def: "Link to additional analysis results performed on the sample MIXS:0000340" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000756 name: extreme unusual properties of heavy metals def: "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field MIXS:0000652" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000757 name: extreme unusual properties of heavy metals method def: "Reference or method used in determining heavy metals MIXS:0000343" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000758 name: extreme unusual properties of AI saturation def: "Aluminum saturation (esp. For tropical soils) MIXS:0000607" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000759 name: extreme unusual properties of AI saturation method def: "Reference or method used in determining Al saturation MIXS:0000324" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000760 name: alkalinity def: "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate MIXS:0000421" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000761 name: alkalinity method def: "Method used for alkalinity measurement MIXS:0000298" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000762 name: alkyl diethers def: "Concentration of alkyl diethers MIXS:0000490" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000763 name: aminopeptidase activity def: "Measurement of aminopeptidase activity MIXS:0000172" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000764 name: ammonium def: "Concentration of ammonium in the sample MIXS:0000427" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000765 name: atmospheric data def: "Measurement of atmospheric data; can include multiple data MIXS:0001097" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000766 name: bacterial carbon production def: "Measurement of bacterial carbon production MIXS:0000173" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000767 name: bacterial production def: "Bacterial production in the water column measured by isotope uptake MIXS:0000683" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000768 name: bacterial respiration def: "Measurement of bacterial respiration in the water column MIXS:0000684" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000769 name: biomass def: "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements MIXS:0000174" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000770 name: bishomohopanol def: "Concentration of bishomohopanol MIXS:0000175" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000771 name: bromide def: "Concentration of bromide MIXS:0000176" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000772 name: calcium def: "Concentration of calcium in the sample MIXS:0000432" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000773 name: carbon nitrogen ratio def: "Ratio of amount or concentrations of carbon to nitrogen MIXS:0000310" [PRIDE:PRIDE] [Term] id: PRIDE:0000774 name: chloride def: "Concentration of chloride in the sample MIXS:0000429" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000775 name: chlorophyll def: "Concentration of chlorophyll MIXS:0000177" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000776 name: conductivity def: "Electrical conductivity of water MIXS:0000692" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000777 name: density def: "Density of the sample, which is its mass per unit volume (aka volumetric mass density) MIXS:0000435" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000778 name: diether lipids def: "Concentration of diether lipids; can include multiple types of diether lipids MIXS:0000178" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000779 name: dissolved carbon dioxide def: "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample MIXS:0000436" [PRIDE:PRIDE] [Term] id: PRIDE:0000780 name: dissolved hydrogen def: "Concentration of dissolved hydrogen MIXS:0000179" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000781 name: dissolved inorganic carbon def: "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter MIXS:0000434" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000784 name: dissolved inorganic nitrogen def: "Concentration of dissolved inorganic nitrogen MIXS:0000698" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000785 name: dissolved inorganic phosphorus def: "Concentration of dissolved inorganic phosphorus in the sample MIXS:0000106" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000786 name: dissolved organic carbon def: "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid MIXS:0000433" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000787 name: dissolved organic nitrogen def: "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 MIXS:0000162" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000788 name: dissolved oxygen def: "Concentration of dissolved oxygen MIXS:0000119" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000789 name: downward PAR def: "Visible waveband radiance and irradiance measurements in the water column MIXS:0000703" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000790 name: fluorescence def: "Raw or converted fluorescence of water MIXS:0000704" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000791 name: glucosidase activity def: "Measurement of glucosidase activity MIXS:0000137" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000792 name: light intensity def: "Measurement of light intensity MIXS:0000706" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000793 name: magnesium def: "Concentration of magnesium in the sample MIXS:0000431" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000794 name: mean friction velocity def: "Measurement of mean friction velocity MIXS:0000498" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000795 name: mean peak friction velocity def: "Measurement of mean peak friction velocity MIXS:0000502" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000796 name: nitrate def: "Concentration of nitrate in the sample MIXS:0000425" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000797 name: nitrite def: "Concentration of nitrite in the sample MIXS:0000426" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000798 name: nitrogen def: "Concentration of nitrogen (total) MIXS:0000504" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000799 name: organic carbon def: "Concentration of organic carbon MIXS:0000508" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000800 name: organic nitrogen def: "Concentration of organic nitrogen MIXS:0000205" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000829 ! Water [Term] id: PRIDE:0000801 name: particulate organic carbon def: "Concentration of particulate organic carbon MIXS:0000515" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000802 name: particulate organic nitrogen def: "Concentration of particulate organic nitrogen MIXS:0000719" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000803 name: petroleum hydrocarbon def: "Concentration of petroleum hydrocarbon MIXS:0000516" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000804 name: phaeopigments def: "Concentration of phaeopigments; can include multiple phaeopigments MIXS:0000180" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000805 name: phosphate def: "Concentration of phosphate MIXS:0000505" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000806 name: phospholipid fatty acid def: "Concentration of phospholipid fatty acids; can include multiple values MIXS:0000181" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000807 name: photon flux def: "Measurement of photon flux MIXS:0000725" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000808 name: potassium def: "Concentration of potassium in the sample MIXS:0000430" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000809 name: pressure def: "Pressure to which the sample is subject to, in atmospheres MIXS:0000412" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000810 name: primary production def: "Measurement of primary production, generally measured as isotope uptake MIXS:0000728" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000811 name: redox potential def: "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential MIXS:0000182" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000812 name: silicate def: "Concentration of silicate MIXS:0000184" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000813 name: size-fraction lower threshold def: "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials smaller than the size threshold are excluded from the sample MIXS:0000735" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000814 name: size-fraction upper threshold def: "Mesh or pore size of the device used to retain the sample. Materials larger than the size threshold are excluded from the sample MIXS:0000736" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000815 name: sodium def: "Sodium concentration in the sample MIXS:0000428" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000816 name: soluble reactive phosphorus def: "Concentration of soluble reactive phosphorus MIXS:0000738" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000817 name: sulfate def: "Concentration of sulfate in the sample MIXS:0000423" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000818 name: sulfide def: "Concentration of sulfide in the sample MIXS:0000424" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000819 name: suspended particulate matter def: "Concentration of suspended particulate matter MIXS:0000741" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000820 name: tidal stage def: "Stage of tide MIXS:0000750" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000821 name: total depth of water column def: "Measurement of total depth of water column MIXS:0000634" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000822 name: total dissolved nitrogen def: "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen MIXS:0000744" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000823 name: total inorganic nitrogen def: "Total inorganic nitrogen content MIXS:0000745" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000824 name: total nitrogen concentration def: "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen MIXS:0000102" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000825 name: total particulate carbon def: "Total particulate carbon content MIXS:0000747" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000826 name: total phosphorus def: "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus MIXS:0000117" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000827 name: turbidity def: "Measure of the amount of cloudiness or haziness in water caused by individual particles MIXS:0000191" [PRIDE:PRIDE] relationship: http://purl.obolibrary.org/obo/BFO_0000050 PRIDE:0000828 ! Soil [Term] id: PRIDE:0000828 name: soil def: "A collection of terms appropriate when collecting samples and sequencing samples obtained from the uppermost layer of Earth's crust, contributed by the Terragenome Consortium" [PRIDE:PRIDE] is_a: ENVO:00010483 ! environmental material [Term] id: PRIDE:0000829 name: water def: "A collection of terms appropriate when collecting samples and sequencing water samples obtained from any aquatic environment" [PRIDE:PRIDE] is_a: ENVO:00002006 ! liquid water [Term] id: PRIDE:0000830 name: Olink Reveal def: "Olink Reveal is an NGS-based proteomics platform that measures approximately 1,000 proteins with high sensitivity from just 4 µL of sample, using standard lab equipment, with a focus on immune and inflammation markers" [PRIDE:PRIDE] is_a: PRIDE:0000654 ! Olink instrument model