diff --git a/NF.csv b/NF.csv index c0169436..0a6bb0bb 100644 --- a/NF.csv +++ b/NF.csv @@ -3,103 +3,104 @@ HPLC,"Frequently referred to simply as HPLC, this form of column chromatography elevated plus maze test,"A method which utilizes an experimental apparatus consisting of four arms, usually two enclosed and two open, in the shape of a plus (+) upon which the test animal can walk. The maze is elevated a set distance, for example 40 to 60 centimeters, above the floor or platform upon which the apparatus sits.",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000262,assay,,,,Elevated_Plus_Maze_Test,Class,Assay,Assay,Behavioral_Assay,,, open field test,"A test utilizing an enclosure consisting of a single area bordered by clear or opaque walls, used to measure movement, exploratory behavior, etc of an experimental subject.",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000258,assay,,,,Open_Field_Test,Class,Assay,Assay,Behavioral_Assay,,, rotarod performance test,"A method that utilizes a device consisting of a rotating rod the speed of which is mechanically driven and precisely controlled, for instance held constant or accelerated. The rotarod test is often used to measure riding time or endurance in order to evaluate balance, motor coordination or grip strength.",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000567,assay,,,,Rotarod_Performance_Test,Class,Assay,Assay,Behavioral_Assay,,, -mRNAcounts,A mRNA profiling assay using digital molecular barcoding technology to quantify target mRNA molecules without the need for amplification.,,,FALSE,Sage Bionetworks,assay,,,,MRNA_Counts,Class,Assay,Assay,RNA_Assay,,, +mRNA counts,A mRNA profiling assay using digital molecular barcoding technology to quantify target mRNA molecules without the need for amplification.,,,FALSE,Sage Bionetworks,assay,,,,MRNA_Counts,Class,Assay,Assay,RNA_Assay,,, high content screen,An image analysis technique combining automated fluorescence microscopy with multi-parameter quantitative image analysis for the large scale study of cells (cellomics).,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0007550,assay,,,,High_Content_Screen,Class,Assay,Assay,Imaging_Assay,,, -Immunocytochemistry,The branch of immunochemistry dealing with cells and cellular activity; the application of immunochemical techniques to cytochemistry.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17731,assay,,,,Immunocytochemistry,Class,Assay,Assay,Immuno_Assay,,, +immunocytochemistry,The branch of immunochemistry dealing with cells and cellular activity; the application of immunochemical techniques to cytochemistry.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17731,assay,,,,Immunocytochemistry,Class,Assay,Assay,Immuno_Assay,,, immunofluorescence,An immunological procedure in which the antibodies are coupled with molecules which fluoresce under ultra violet (UV) light. This makes them particularly suitable for detection of specific antigens in tissues or on cells.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17370,assay,,,,Immunofluorescence,Class,Assay,Assay,Immuno_Assay,,, autoradiography,A radioactivity detection technique using X- ray film to visualize molecules or fragments of molecules that have been radioactively labeled.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0000716,assay,,,,Autoradiography,Class,Assay,Assay,Radio_Assay,,, reporter gene assay,"Reporter gene assay measures the gene expression from a reporter gene. The reporter gene is inserted under the control of a foreign promoter or an artificial regulatory element of interest. Reporters include luciferase, beta galactosidase, beta lactamase, chloramphenicol acetyl transferase, or a fluorescent protein.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002082,assay,,,,Reporter_Gene_Assay,Class,Assay,Assay,RNA_Assay,,, electrochemiluminescence,"A method in which electromagnetic radiation, in the form of light emission, is generated from an electrochemical reaction in a solution.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C111193,assay,,,,Electrochemiluminescence,Class,Assay,Assay,RNA_Assay,,, -Real Time PCR,An application of PCR that measures the products generated during each cycle of the polymerase chain reaction process in order to determine the starting amount of template in the reaction.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C51962,assay,,,,Real_Time_PCR,Class,Assay,Assay,RNA_Assay,,, +real-time PCR,An application of PCR that measures the products generated during each cycle of the polymerase chain reaction process in order to determine the starting amount of template in the reaction.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C51962,assay,,,,Real_Time_PCR,Class,Assay,Assay,RNA_Assay,,, in vivo tumor growth,"The growth of a tumor measured using calipers, ruler, or another similar measurement device. See also """"in vivo bioluminescence"""".",,,FALSE,Sage Bionetworks,assay,,,,In_Vivo_Tumor_Growth,Class,Assay,Assay,Volume_Measurement_Assay,,, -Blood Chemistry Measurement,The determination of the measured concentrations of chemical constituents of the blood by assay in a clinical laboratory.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C47868,assay,,,,Blood_Chemistry_Measurement,Class,Assay,Assay,Clinical_Assay_Template,,, +blood chemistry measurement,The determination of the measured concentrations of chemical constituents of the blood by assay in a clinical laboratory.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C47868,assay,,,,Blood_Chemistry_Measurement,Class,Assay,Assay,Clinical_Assay_Template,,, in vivo bioluminescence,An imaging assay that allows detection of bioluminescence from a living organism or organisms.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0000651,assay,,,,In_Vivo_Bioluminescence,Class,Assay,Assay,Imaging_Assay,,, immunohistochemistry,An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001986,assay,,,,Immunohistochemistry,Class,Assay,Assay,Immuno_Assay,,, -NOMe-Seq,Nucleosome Occupancy and Methylome Sequencing,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C106053,assay,,,,NOMe-Seq,Class,Assay,Assay,Epigenetics_Assay,,, +NOMe-seq,Nucleosome Occupancy and Methylome Sequencing,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C106053,assay,,,,NOMe-Seq,Class,Assay,Assay,Epigenetics_Assay,,, FIA-MSMS,Flow injection analysis - tandem mass spectrometer,,,FALSE,https://www.ncbi.nlm.nih.gov/pubmed/28667829,assay,,,,FIA-MSMS,Class,Assay,Assay,Proteomics_Assay,,, -UPLC-MSMS,Ultra performance liquid chromatography - tandem mass spectrometer.,,,FALSE,https://www.wur.nl/en/show/Ultra-performance-liquid-chromatography-tandem-mass-spectrometer-UPLCMSMS.htm,assay,,,,UPLC-MSMS,Class,Assay,Assay,Proteomics_Assay,,, -HPLC-MSMS,"An analytical technique wherein high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C120691,assay,,,,HPLC-MSMS,Class,Assay,Assay,Proteomics_Assay,,, +ultra high-performance liquid chromatography/tandem mass spectrometry,"UPLC-MSMS is an analytical technique wherein ultra-high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C122176,assay,,,,Ultra_High-performance_Liquid_Chromatography_Tandem_Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, +high-performance liquid chromatography/tandem mass spectrometry,"HPLC-MSMS is an analytical technique wherein high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C120691,assay,,,,High-performance_Liquid_Chromatography_Tandem_Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, liquid chromatography-electrochemical detection,"A liquid chromatography method that is sensitive to compounds which can be either reduced or oxidised. The mobile phase passes directly over the working electrode, which is set to the specific potential required for oxidation or reduction. The current produced is then measured.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0001746,assay,,,,Liquid_Chromatography-Electrochemical_Detection,Class,Assay,Assay,Proteomics_Assay,,, -rnaSeq,RNA Sequencing measurements,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001271,assay,,,,RNA-Seq,Class,Assay,Assay,RNA_Assay,,, -mirnaSeq,Small RNA measurements collected from RNA-Seq experiments,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002112,assay,,,,MiRNA-Seq,Class,Assay,Assay,RNA_Assay,,, -LC-MSMS,A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000701,assay,,,,LC-MSMS,Class,Assay,Assay,Proteomics_Assay,,, -LC-MS,A method where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterised by their mass-to-charge ratio and relative abundance,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000524,assay,,,,LC-MS,Class,Assay,Assay,Proteomics_Assay,,, -lncrnaSeq,Long non-coding RNA measurements collected from RNA-Seq experiments,,,FALSE,,assay,,,,LCRNA-Seq,Class,Assay,Assay,RNA_Assay,,, -Whole Exome Sequencing,A procedure that can determine the DNA sequence for all of the exons in an individual.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C101295,assay,,,,Whole_Exome_Sequencing,Class,Assay,Assay,DNA_Assay,,, +RNA-seq,RNA Sequencing measurements,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001271,assay,,,,RNA-Seq,Class,Assay,Assay,RNA_Assay,,, +miRNA-seq,Small RNA measurements collected from RNA sequencing experiments,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002112,assay,,,,MiRNA-Seq,Class,Assay,Assay,RNA_Assay,,, +liquid chromatography/tandem mass spectrometry,"LC-MSMS is an analytical technique wherein liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C122168,assay,,,,Liquid_Chromatography_Tandem_Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, +liquid chromatography/mass spectrometry,"LC-MS is a hyphenated technique, combining the separation power of liquid chromatography (LC), an analytical chromatographic technique for separating ions or molecules dissolved in a solvent, with the detection power of mass spectrometry(MS), a technique to separate gas phase ions according their m/z (mass to charge ratio) value. Used for drug screening, pharmacology studies, environmental analyses and forensics.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C18475,assay,,,,Liquid_Chromatography_Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, +lncRNA-seq,Long non-coding RNA measurements collected from RNA-Seq experiments,,,FALSE,,assay,,,,LCRNA-Seq,Class,Assay,Assay,RNA_Assay,,, +whole exome sequencing,A procedure that can determine the DNA sequence for all of the exons in an individual.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C101295,assay,,,,Whole_Exome_Sequencing,Class,Assay,Assay,DNA_Assay,,, Sanger sequencing,"A DNA sequencing technique in which a mixture of deoxynucleosidetriphosphates (dNTPs) and chain-terminating dNTPs, which are radioactively or fluorescently labeled, are combined within the reaction mixture. Once the reaction is complete, the DNA strands are separated by size, and the labeled chain terminating dNTPs can be read in sequence by the investigator or by a machine.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C19641,assay,,,,Sanger_Sequencing,Class,Assay,Assay,DNA_Assay,,, -ChIPSeq,Chromatin immuno-precipitation followed by sequencing,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000716,assay,,,,ChIP-Seq,Class,Assay,Assay,Epigenetics_Assay,,, -rnaArray,RNA measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001463,assay,,,,RNA_Array,Class,Assay,Assay,RNA_Assay,,, -snpArray,SNP measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001204,assay,,,,SNP_Array,Class,Assay,Assay,DNA_Assay,,, -methylationArray,Methylation data captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001332,assay,,,,Methylation_Array,Class,Assay,Assay,Epigenetics_Assay,,, -mirnaArray,microRNA measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001335,assay,,,,MiRNA_Array,Class,Assay,Assay,RNA_Assay,,, -bisulfiteSeq,Methylation data captured by sequencing of DNA treated by a bisulfite-based chemical process,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000748,assay,,,,Bisulfite_Seq,Class,Assay,Assay,Epigenetics_Assay,,, -ATACSeq,Open chromatin regions measured by sequencing DNA after assay for transposase-accessible chromatin (ATAC) treatment,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002039,assay,,,,ATAC_Seq,Class,Assay,Assay,Epigenetics_Assay,,, +ChIP-seq,Chromatin immuno-precipitation followed by sequencing,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000716,assay,,,,ChIP-Seq,Class,Assay,Assay,Epigenetics_Assay,,, +RNA array,RNA measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001463,assay,,,,RNA_Array,Class,Assay,Assay,RNA_Assay,,, +SNP array,SNP measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001204,assay,,,,SNP_Array,Class,Assay,Assay,DNA_Assay,,, +methylation array,Methylation data captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001332,assay,,,,Methylation_Array,Class,Assay,Assay,Epigenetics_Assay,,, +miRNA array,microRNA measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001335,assay,,,,MiRNA_Array,Class,Assay,Assay,RNA_Assay,,, +bisulfite sequencing,Methylation data captured by sequencing of DNA treated by a bisulfite-based chemical process,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000748,assay,,,,Bisulfite_Seq,Class,Assay,Assay,Epigenetics_Assay,,, +ATAC-seq,Open chromatin regions measured by sequencing DNA after assay for transposase-accessible chromatin (ATAC) treatment,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002039,assay,,,,ATAC_Seq,Class,Assay,Assay,Epigenetics_Assay,,, HI-C,Chromatin interactions detected by HI-C protocol,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0007693,assay,,,,HI-C,Class,Assay,Assay,Epigenetics_Assay,,, -errBisulfiteSeq,Data for enriched reduced representation bisulfite sequencing data,,,FALSE,,assay,,,,Err_Bisulfite_Seq,Class,Assay,Assay,Bisulfite_Seq,,, -ISOSeq,Full isoform sequencing,,,FALSE,,assay,,,,ISO-Seq,Class,Assay,Assay,RNA_Assay,,, -westernBlot,A multistep process in which a mixture of proteins is separated by gel electrophoresis,,,FALSE,http://purl.obolibrary.org/obo/MMO_0000338,assay,,,,Western_Blot,Class,Assay,Assay,Proteomics_Assay,,, -wholeGenomeSeq,Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time,,,FALSE,http://edamontology.org/topic_3673,assay,,,,Whole_Genome_Seq,Class,Assay,Assay,DNA_Assay,,, -polymeraseChainReaction,"A rapid technique for in vitro amplification of specific DNA or RNA sequences, allowing small quantities of short sequences to be analyzed without cloning",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000459,assay,,,,Polymerase_Chain_Reaction,Class,Assay,Assay,RNA_Assay,,, -cellViabilityAssay,This assay type measures the cellular state of living or dying by measuring an indicator of life or death,,,FALSE,http://www.bioassayontology.org/bao#BAO_0003009,assay,,,,Cell_Viability_Assay,Class,Assay,Assay,Cell_Assay,,, +ERR bisulfite sequencing,Enhanced reduced representation bisulfite sequencing (ERRBS) ,,,FALSE,,assay,,,,Err_Bisulfite_Seq,Class,Assay,Assay,Bisulfite_Seq,,, +ISO-seq,Full isoform sequencing,,,FALSE,,assay,,,,ISO-Seq,Class,Assay,Assay,RNA_Assay,,, +western blot,A multistep process in which a mixture of proteins is separated by gel electrophoresis,,,FALSE,http://purl.obolibrary.org/obo/MMO_0000338,assay,,,,Western_Blot,Class,Assay,Assay,Proteomics_Assay,,, +whole genome sequencing,Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time,,,FALSE,http://edamontology.org/topic_3673,assay,,,,Whole_Genome_Seq,Class,Assay,Assay,DNA_Assay,,, +polymerase chain reaction,"A rapid technique for in vitro amplification of specific DNA or RNA sequences, allowing small quantities of short sequences to be analyzed without cloning",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000459,assay,,,,Polymerase_Chain_Reaction,Class,Assay,Assay,RNA_Assay,,, +cell viability assay,This assay type measures the cellular state of living or dying by measuring an indicator of life or death,,,FALSE,http://www.bioassayontology.org/bao#BAO_0003009,assay,,,,Cell_Viability_Assay,Class,Assay,Assay,Cell_Assay,,, 2D Incucyte,Cell viability assay on a 2D monolayer model.,,,FALSE,,assay,,,,2D_Incucyte_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 2D CellTiter-Glo,Cell viability assay based on detection of ATP.,,,FALSE,https://www.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?catNum=G9241,assay,,,,2D_Cell_Titer_Glo_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 3D microtissue viability,Cell viability assay on a 3D microtissue model.,,,FALSE,https://www.ncbi.nlm.nih.gov/books/NBK343426/,assay,,,,3D_Microtissue_Viability_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 2D AlamarBlue fluorescence,"Cell viability assay based on detection of AlamarBlue (resazurin). Living cells reduce blue, non-fluorescent resazurin to the red, fluorescent molecule resorufin. The amount of fluorescence or absorbance is proportional to the number of living cells and corresponds to the cell’s metabolic activity. For the fluorescence-based assay, color change and fluorescence can be detected using 560/590 nm (excitation/emission).",,,FALSE,https://www.thermofisher.com/us/en/home/life-science/cell-analysis/fluorescence-microplate-assays/microplate-assays-cell-viability/alamarblue-assay-cell-viability.html,assay,,,,2D_AlamarBlue_Fluorescence,Class,Assay,Assay,Cell_Viability_Assay,,, 2D AlamarBlue absorbance,"Cell viability assay based on detection of AlamarBlue (resazurin). Living cells reduce blue, non-fluorescent resazurin to the red, fluorescent molecule resorufin. The amount of fluorescence or absorbance is proportional to the number of living cells and corresponds to the cell’s metabolic activity. For the absorbance-based assay, absorbance can be read at 570 nm.",,,FALSE,https://www.thermofisher.com/us/en/home/life-science/cell-analysis/fluorescence-microplate-assays/microplate-assays-cell-viability/alamarblue-assay-cell-viability.html,assay,,,,2D_AlamarBlue_Absorbance,Class,Assay,Assay,Cell_Viability_Assay,,, in vivo PDX viability,Assay to assess viability using PDX model.,,,FALSE,,assay,,,,In_Vivo_PDX_Viability_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, -atomicForceMicroscopy,Microscopy which uses a sharp spike (known as a 'tip') mounted on the end of a cantilever to scan the surface of the specimen,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000113,assay,,,,Atomic_Force_Microscopy,Class,Assay,Assay,Imaging_Assay,,, -brightfieldMicroscopy,Microscopy where the specimen is illuminated with light transmitted from a source on the opposite side of the specimen from the objective,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000104,assay,,,,Brightfield_Microscopy,Class,Assay,Assay,Imaging_Assay,,, -tractionForceMicroscopy,An experimental method for determining the tractions on the surface of a biological cell by obtaining measurements of the surrounding displacement field within an in vitro extracellular matrix (ECM),,,FALSE,https://en.wikipedia.org/wiki/Traction_force_microscopy,assay,,,,Traction_Force_Microscopy,Class,Assay,Assay,Imaging_Assay,,, -Phase-Contrast Microscopy,A simple non-quantitative form of interference microscopy of great utility in visualising live cells. Small differences in optical path length due to differences in refractive index and thickness of structures are visualised as differences in light intensity.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16857,assay,,,,Phase-Contrast_Microscopy,Class,Assay,Assay,Imaging_Assay,,, -nextGenerationTargetedSequencing,A type of next generation sequencing in which specific genes or portions of genes are targeted for sequencing using amplicon-based workflow.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C130177,assay,,,,NextGeneration_Targeted_Seq,Class,Assay,Assay,DNA_Assay,,, +atomic force microscopy,Microscopy which uses a sharp spike (known as a 'tip') mounted on the end of a cantilever to scan the surface of the specimen,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000113,assay,,,,Atomic_Force_Microscopy,Class,Assay,Assay,Imaging_Assay,,, +brightfield microscopy,Microscopy where the specimen is illuminated with light transmitted from a source on the opposite side of the specimen from the objective,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000104,assay,,,,Brightfield_Microscopy,Class,Assay,Assay,Imaging_Assay,,, +traction force microscopy,An experimental method for determining the tractions on the surface of a biological cell by obtaining measurements of the surrounding displacement field within an in vitro extracellular matrix (ECM),,,FALSE,https://en.wikipedia.org/wiki/Traction_force_microscopy,assay,,,,Traction_Force_Microscopy,Class,Assay,Assay,Imaging_Assay,,, +phase-contrast microscopy,A simple non-quantitative form of interference microscopy of great utility in visualising live cells. Small differences in optical path length due to differences in refractive index and thickness of structures are visualised as differences in light intensity.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16857,assay,,,,Phase-Contrast_Microscopy,Class,Assay,Assay,Imaging_Assay,,, +next generation targeted sequencing,A type of next generation sequencing in which specific genes or portions of genes are targeted for sequencing using amplicon-based workflow.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C130177,assay,,,,NextGeneration_Targeted_Seq,Class,Assay,Assay,DNA_Assay,,, MIB/MS,Kinomics assay using multiplexed kinase inhibitor beads and mass spectrometry (MIB/MS),,,FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328787/,assay,,,,MIB_MS,Class,Assay,Assay,Proteomics_Assay,,, -scCGIseq,"A method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs",,,FALSE,https://www.ncbi.nlm.nih.gov/pubmed/28126923,assay,,,,ScCGI_Seq,Class,Assay,Assay,Epigenetics_Assay,,, +scCGI-seq,"A method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs",,,FALSE,https://www.ncbi.nlm.nih.gov/pubmed/28126923,assay,,,,ScCGI_Seq,Class,Assay,Assay,Epigenetics_Assay,,, MudPIT,MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry,,,FALSE,http://purl.obolibrary.org/obo/MI_0658,assay,,,,MudPIT,Class,Assay,Assay,Proteomics_Assay,,, questionnaire,"A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0001000,assay,,,,Questionnaire,Class,Assay,Assay,Behavioral_Assay,,, DNA optical mapping,Fluorescent imaging of linearly extended DNA molecules to probe information patterns along the molecules,,,FALSE,https://doi.org/10.1016/j.copbio.2013.01.009,assay,,,,DNA_Optical_Mapping,Class,Assay,Assay,Imaging_Assay,,, -oxBS-Seq,Oxidative bisulfite sequencing (oxBS-Seq) to map 5-methylcytosine and 5-hydroxymethylcytosine,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008840,assay,,,,OxBS-Seq,Class,Assay,Assay,Epigenetics_Assay,,, -Ribo-Seq,Ribosome profiling (Ribo-Seq).,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008891,assay,,,,Ribo-Seq,Class,Assay,Assay,RNA-Seq,,, -Positron Emission Tomography,A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17007,assay,,,,Positron_Emission_Tomography,Class,Assay,Assay,Imaging_Assay,,, +oxBS-seq,Oxidative bisulfite sequencing (oxBS-Seq) to map 5-methylcytosine and 5-hydroxymethylcytosine,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008840,assay,,,,OxBS-Seq,Class,Assay,Assay,Epigenetics_Assay,,, +ribo-seq,Ribosome profiling (Ribo-Seq).,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008891,assay,,,,Ribo-Seq,Class,Assay,Assay,RNA-Seq,,, +positron emission tomography,A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17007,assay,,,,Positron_Emission_Tomography,Class,Assay,Assay,Imaging_Assay,,, RPPA,Reverse phase protein array (RPPA) is a an assay that measures multiple protein expression levels in a large number of biological samples simultaneously using high quality antibodies,,,FALSE,http://www.bioassayontology.org/bao#BAO_0010030,assay,,,,RPPA,Class,Assay,Assay,Proteomics_Assay,,, ELISA,"A highly sensitive technique for detecting and measuring antigens or antibodies in a solution; the solution is run over a surface to which immobilized antibodies specific to the substance have been attached, and if the substance is present, it will bind to the antibody layer, and its presence is verified and visualized with an application of antibodies that have been tagged in some way.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16553,assay,,,,ELISA,Class,Assay,Assay,Proteomics_Assay,,, -LTP,Any measurable or observable characteristic related to the persistent robust synaptic response induced by synchronous stimulation of pre- and postsynaptic cells.,,,FALSE,http://purl.obolibrary.org/obo/VT_0002207,assay,,,,LTP,Class,Assay,Assay,Electrophysiology_Assay,,, -LFP,An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002189,assay,,,,LFP,Class,Assay,Assay,Electrophysiology_Assay,,, +long term potentiation assay,A measure of the persistent robust synaptic response induced by synchronous stimulation of pre- and postsynaptic cells.,,,FALSE,http://purl.obolibrary.org/obo/VT_0002207,assay,,,,Long_Term_Potentiation_Assay,Class,Assay,Assay,Electrophysiology_Assay,,, +local field potential recording,An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002189,assay,,,,Local_Field_Potential_Recording,Class,Assay,Assay,Electrophysiology_Assay,,, whole-cell patch clamp,"A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002178,assay,,,,Whole-cell_Patch_Clamp,Class,Assay,Assay,Cell_Assay,,, sandwich ELISA,"The sandwich ELISA measures the amount of antigen between two layers of antibodies. The antigens to be measured must contain at least two antigenic sites, capable of binding to antibody, since at least two antibodies act in the sandwich. So sandwich assays are restricted to the quantitation of multivalent antigens such as proteins or polysaccharides. Sandwich ELISAs for quantitation of antigens are especially valuable when the concentration of antigens is low and/or they are contained in high concentrations of contaminating protein.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/bao/terms?iri=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0002421,assay,,,,Sandwich_ELISA,Class,Assay,Assay,ELISA,,, -Laser Speckle Imaging,"A noninvasive, non-scanning optical imaging technique that provides full-field visualization of blood flow to the tissue being imaged, which provides information about tissue perfusion and the efficiency of disease treatment.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C116492,assay,,,,Laser_Speckle_Imaging,Class,Assay,Assay,Imaging_Assay,,, -Genotyping,The determination of the DNA sequence of an individual.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C45447,assay,,,,Genotyping_Assay,Class,Assay,Assay,DNA_Assay,,, +laser speckle imaging,"A noninvasive, non-scanning optical imaging technique that provides full-field visualization of blood flow to the tissue being imaged, which provides information about tissue perfusion and the efficiency of disease treatment.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C116492,assay,,,,Laser_Speckle_Imaging,Class,Assay,Assay,Imaging_Assay,,, +genotyping,The determination of the DNA sequence of an individual.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C45447,assay,,,,Genotyping_Assay,Class,Assay,Assay,DNA_Assay,,, TMT quantitation,"An isobaric labeling technique that uses tags containing four regions with the same total molecular weights and structure, so that during chromatographic or electrophoretic separation and in single MS mode, molecules labelled with different tags are indistinguishable.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0002175,assay,,,,TMT_Quantitation,Class,Assay,Assay,Proteomics_Assay,,, +mass spectrometry,"A generic mass spectrometry assay that allows identification and amount of peptide or protein materials.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0000708,assay,,,,Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, label free mass spectrometry,"A mass spectrometry assay that allows for measurement for endogenous targets in live cell assays, and eliminates the need for tags, dyes, or specialized reagents or engineered cells.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0000708,assay,,,,Label_Free_Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, cell count,A procedure to determine the number of cells in a sample. Also used to mean the result of such a procedure.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C48938,assay,,,,Cell_Count,Class,Assay,Assay,Cell_Assay,,, -immunoAssay,Generic immunology assay,,immunoAssayType,FALSE,,assay,,,,Immuno_Assay,Class,Assay,Assay,Assay,,, -Conventional MRI,"Magnetic resonance imaging using standard protocols for high resolution structural and anatomic characterization, including T1 weighted, T2 weighted, fluid attenuated inversion recovery (FLAIR), and gadolinium-enhanced sequences. [ NCI ]",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C175525,assay,,,,Conventional_MRI,Class,Assay,Assay,MRI_Assay,,, -Functional MRI,The principle of functional MRI imaging is to take a series of images of an organ in quick succession and to statistically analyze the images for differences among them. Most commonly used in studies of brain function. [ NCI ],,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17958,assay,,,,Functional_MRI,Class,Assay,Assay,MRI_Assay,,, -Magnetic Resonance Spectroscopy,Detection and measurement of the resonant spectra of molecular species in a tissue or sample.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16810,assay,,,,Magnetic_Resonance_Spectroscopy,Class,Assay,Assay,Radio_Assay,,, -FTIR Spectroscopy,"Fourier transform infrared (FTIR) spectroscopy is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid or gas. An FTIR spectrometer simultaneously collects high-resolution spectral data over a wide spectral range.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000636,assay,,,,FTIR_Spectroscopy,Class,Assay,Assay,Proteomics_Assay,,, +immunoassay,Generic immunology assay,,immunoAssayType,FALSE,,assay,,,,Immuno_Assay,Class,Assay,Assay,Assay,,, +conventional MRI,"Magnetic resonance imaging using standard protocols for high resolution structural and anatomic characterization, including T1 weighted, T2 weighted, fluid attenuated inversion recovery (FLAIR), and gadolinium-enhanced sequences. [ NCI ]",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C175525,assay,,,,Conventional_MRI,Class,Assay,Assay,MRI_Assay,,, +functional MRI,The principle of functional MRI imaging is to take a series of images of an organ in quick succession and to statistically analyze the images for differences among them. Most commonly used in studies of brain function. [ NCI ],,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17958,assay,,,,Functional_MRI,Class,Assay,Assay,MRI_Assay,,, +magnetic resonance spectroscopy,Detection and measurement of the resonant spectra of molecular species in a tissue or sample.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16810,assay,,,,Magnetic_Resonance_Spectroscopy,Class,Assay,Assay,Radio_Assay,,, +FTIR spectroscopy,"Fourier transform infrared (FTIR) spectroscopy is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid or gas. An FTIR spectrometer simultaneously collects high-resolution spectral data over a wide spectral range.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000636,assay,,,,FTIR_Spectroscopy,Class,Assay,Assay,Proteomics_Assay,,, rheometry,The study of the flow of fluids which cannot be defined by a single value of viscosity. Rheometry (synonym: rheology) is the measurement of the relationship between deformation and stress for these liquids. [ https://orcid.org/0000-0002-0640-0422 ],,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000915,assay,,,,Rheometry,Class,Assay,Assay,Assay,,, -Gel filtration chromatography,"Gel filtration chromatography (synonym: gel permeation chromatography - GPC) is a type of size-exclusion chromatography (SEC), that separates analytes on the basis of size, typically in organic solvents. The technique is often used for the analysis of polymers.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0001011,assay,,,,Gel_Filtration_Chromatography,Class,Assay,Assay,Proteomics_Assay,,, +gel filtration chromatography,"Gel filtration chromatography (synonym: gel permeation chromatography - GPC) is a type of size-exclusion chromatography (SEC), that separates analytes on the basis of size, typically in organic solvents. The technique is often used for the analysis of polymers.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0001011,assay,,,,Gel_Filtration_Chromatography,Class,Assay,Assay,Proteomics_Assay,,, differential scanning calorimetry,"Differential scanning calorimetry (DSC) is the measurement of thermodynamic parameters (e.g. enthalpy) during a chemical or biochemical reaction of both a sample and a reference, by the known variation (step-wise or linear) of one variable, whilst a second is kept constant.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000684,assay,,,,Differential_Scanning_Calorimetry,Class,Assay,Assay,Assay,,, -singleMolecule,An experiment in which a single molecule was used in an assay,,,FALSE,,drugScreenType,,,,Single_Molecule_Drug_Screen,Class,Assay,Assay,Drug_Screen,,, -smallMoleculeLibraryScreen,"High throughput sample analysis of small molecules for purpose such as drug discovery, or biochemical, genetic or pharmacological tests.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0001726,drugScreenType,,,,Small_Molecule_Library_Screen,Class,Assay,Assay,Drug_Screen,,, -combinationLibraryScreen,High throughput sample analysis of collections of compounds that provide a variety of chemically diverse structures that can be used to identify structure types that have affinity with pharmacological targets.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0001686,drugScreenType,,,,Combination_Library_Screen,Class,Assay,Assay,Drug_Screen,,, -combinationScreen,,,,FALSE,,drugScreenType,,,,Combination_Screen,Class,Assay,Assay,Drug_Screen,,, -compoundScreen,,,,FALSE,,assay,,,,Compound_Screen,Class,Assay,Assay,Drug_Screen,,, +single molecule drug screen assay,An experiment in which a single molecule was used in an assay,,,FALSE,,drugScreenType,,,,Single_Molecule_Drug_Screen,Class,Assay,Assay,Drug_Screen,,, +small molecule library screen,"High throughput sample analysis of small molecules for purpose such as drug discovery, or biochemical, genetic or pharmacological tests.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0001726,drugScreenType,,,,Small_Molecule_Library_Screen,Class,Assay,Assay,Drug_Screen,,, +combination library screen,High throughput sample analysis of collections of compounds that provide a variety of chemically diverse structures that can be used to identify structure types that have affinity with pharmacological targets.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0001686,drugScreenType,,,,Combination_Library_Screen,Class,Assay,Assay,Drug_Screen,,, +combination screen,,,,FALSE,,drugScreenType,,,,Combination_Screen,Class,Assay,Assay,Drug_Screen,,, +compound screen,,,,FALSE,,assay,,,,Compound_Screen,Class,Assay,Assay,Drug_Screen,,, array,,,,FALSE,,assay,,,,Array,Class,Assay,Assay,Assay,,, -Single Cell RNA Sequencing,A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C171152,assay,,,,ScRNA_Seq,Class,Assay,Assay,RNA-Seq,,, +single-cell RNA-seq,A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C171152,assay,,,,ScRNA_Seq,Class,Assay,Assay,RNA-Seq,,, spatial transcriptomics,"assay that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections",,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008994,assay,,,,Spatial_Transcriptomics,Class,Assay,Assay,RNA-Seq,,, -Massively Parallel Reporter Assay,An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002675,assay,,,,Massively_Parallel_Reporter_Assay,Class,Assay,Assay,Reporter_Gene_Assay,,, +massively parallel reporter assay,An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002675,assay,,,,Massively_Parallel_Reporter_Assay,Class,Assay,Assay,Reporter_Gene_Assay,,, Riccardi and Ablon scales,"The Riccardi and Ablon scales score severity and visibility of disease, respectively, and are commonly used as a combined assessment for NF1 patients in clinical settings. See https://doi.org/10.1001/archderm.137.11.1421 for example usage.",,,FALSE,https://doi.org/10.1001/archderm.137.11.1421,assay,,,,Riccardi_Ablon_Scales,Class,Assay,Assay,Clinical_Assay,,, -Spatial Frequency Domain Imaging,"Spatial Frequency Domain Imaging (SFDI) is a non-contact, depth-varying and wide-field optical imaging technique for measuring optical properties in a wide field-of-view on a pixel-by-pixel basis. Relevant applications include including burn assessment, skin tissue evaluation, tumor tissue detection, brain tissue monitoring.",,,FALSE,https://doi.org/10.3390/photonics8050162,assay,,,,Spatial_Frequency_Domain_Imaging,Class,Assay,Assay,Imaging_Assay,,,Note that term has no matches in OLS as of June 2022. -Optical Coherence Tomography,"Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C20828,assay,,,,Optical_Coherence_Tomography,Class,Assay,Assay,Imaging_Assay,,, +spatial frequency domain imaging,"Spatial Frequency Domain Imaging (SFDI) is a non-contact, depth-varying and wide-field optical imaging technique for measuring optical properties in a wide field-of-view on a pixel-by-pixel basis. Relevant applications include including burn assessment, skin tissue evaluation, tumor tissue detection, brain tissue monitoring.",,,FALSE,https://doi.org/10.3390/photonics8050162,assay,,,,Spatial_Frequency_Domain_Imaging,Class,Assay,Assay,Imaging_Assay,,,Note that term has no matches in OLS as of June 2022. +optical coherence tomography,"Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C20828,assay,,,,Optical_Coherence_Tomography,Class,Assay,Assay,Imaging_Assay,,, CUT&RUN,"Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. (doi:10.7554/eLife.21856)",,,FALSE,,assay,,,,CUT_RUN,Class,Assay,Assay,Epigenetics_Assay,,, -3D Imaging,"Technique to produce 3D images to visualize important structures in great detail. To produce 3D images, many scans are made, and then combined by computers to produce a 3D model, which can then be manipulated. 3D ultrasounds are produced using a somewhat similar technique.",,Assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C18485,assay,,,,3D_Imaging,Class,Assay,Assay,Imaging_Assay,,, -High Frequency Ultrasound,"High frequency ultrasound (HFUS) is an imaging modality that can give greater resolution of surface changes in skin (review in PMID:24583666)",,Assay,FALSE,,assay,,,,High_Frequency_Ultrasound,Class,Assay,Assay,Imaging_Assay,,, -Dynamic Light Scattering,"Dynamic Light Scattering (DLS), also known as photocorrelation spectroscopy, is a method for determining the size distribution of a sample of small particles in solution by illuminating the sample with a light source (usually a laser) and measuring the time-dependent fluctuations in the intensity of the scattered light caused by Brownian motion.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000167,assay,,,,Dynamic_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,, -Static Light Scattering,"Static Light Scattering is a method for determining structure by measuring the total or time-averaged scattering intensity of scattered visible light as a function of angle.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000180,assay,,,,Static_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,, -Light Scattering Assay,"A method for determining structure by measuring the change in direction or energy of scattered visible light. Light is scattered by the electrons surrounding the atomic nuclei in the sample.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000166,assay,,,,Light_Scattering_Assay,Class,Assay,Assay,Spectroscopy,,, +3D imaging,"Technique to produce 3D images to visualize important structures in great detail. To produce 3D images, many scans are made, and then combined by computers to produce a 3D model, which can then be manipulated. 3D ultrasounds are produced using a somewhat similar technique.",,Assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C18485,assay,,,,3D_Imaging,Class,Assay,Assay,Imaging_Assay,,, +high frequency ultrasound,"High frequency ultrasound (HFUS) is an imaging modality that can give greater resolution of surface changes in skin (review in PMID:24583666)",,Assay,FALSE,,assay,,,,High_Frequency_Ultrasound,Class,Assay,Assay,Imaging_Assay,,, +dynamic light scattering,"Dynamic Light Scattering (DLS), also known as photocorrelation spectroscopy, is a method for determining the size distribution of a sample of small particles in solution by illuminating the sample with a light source (usually a laser) and measuring the time-dependent fluctuations in the intensity of the scattered light caused by Brownian motion.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000167,assay,,,,Dynamic_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,, +static light scattering,"Static Light Scattering is a method for determining structure by measuring the total or time-averaged scattering intensity of scattered visible light as a function of angle.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000180,assay,,,,Static_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,, +light scattering assay,"A method for determining structure by measuring the change in direction or energy of scattered visible light. Light is scattered by the electrons surrounding the atomic nuclei in the sample.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000166,assay,,,,Light_Scattering_Assay,Class,Assay,Assay,Spectroscopy,,, flow cytometry,"A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution",,,FALSE,http://purl.obolibrary.org/obo/OBI_0000916,assay,,,,Flow_Cytometry_Assay,Class,Assay,Assay,Assay,,, -Pattern electroretinogram,"Pattern electroretinogram (PERG) is an electrophysiologic ophthalmologic test that provides non-invasive objective, quantitative measurement of central retinal function. PERG is the retinal response to a pattern-reversing, black-and-white checkerboard or stripped stimulus. The PERG assesses both macular and retinal ganglion cell electrical activity and can help differentiate between diseases of macular versus optic nerve dysfunction.",,,FALSE,https://www.ncbi.nlm.nih.gov/books/NBK560641,assay,,,,Pattern_Electroretinogram,Class,Assay,Assay,Assay,,, -Optokinetic reflex assay,"The optokinetic reflex (OKR), which serves to stabilize a moving image on the retina, is a behavioral response that has many favorable attributes as a test of CNS function. The OKR requires no training, assesses the function of diverse CNS circuits, can be induced repeatedly with minimal fatigue or adaptation, and produces an electronic record that is readily and objectively quantifiable.",,,FALSE,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002055,assay,,,,SUSHI,Class,Assay,Assay,Assay,,, +pattern electroretinogram,"Pattern electroretinogram (PERG) is an electrophysiologic ophthalmologic test that provides non-invasive objective, quantitative measurement of central retinal function. PERG is the retinal response to a pattern-reversing, black-and-white checkerboard or stripped stimulus. The PERG assesses both macular and retinal ganglion cell electrical activity and can help differentiate between diseases of macular versus optic nerve dysfunction.",,,FALSE,https://www.ncbi.nlm.nih.gov/books/NBK560641,assay,,,,Pattern_Electroretinogram,Class,Assay,Assay,Assay,,, +optokinetic reflex assay,"The optokinetic reflex (OKR), which serves to stabilize a moving image on the retina, is a behavioral response that has many favorable attributes as a test of CNS function. The OKR requires no training, assesses the function of diverse CNS circuits, can be induced repeatedly with minimal fatigue or adaptation, and produces an electronic record that is readily and objectively quantifiable.",,,FALSE,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002055,assay,,,,SUSHI,Class,Assay,Assay,Assay,,, SUSHI,"Fast super-resolution method that exploits sparsity in the underlying vasculature and statistical independence within the measured signals to detect slow-flowing blood, facilitating noninvasive perfusion measurements.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/30295619/,assay,,,,Optokinetic_Reflex_Assay,Class,Assay,Assay,Assay,,, 3D confocal imaging,"Confocal microscopy with 3D reconstruction of the sample tissue.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/34331281,assay,,,,3D_Confocal_Imaging,Class,Assay,Assay,Imaging_Assay,,, 3D electron microscopy,"Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,3D_Electron_Microscopy,Class,Assay,Assay,Imaging_Assay,,, @@ -107,7 +108,18 @@ cell competition,"An assay in which two or more labeled populations of cells or body size trait measurement,"Any measurable or observable characteristic related to the overall physical magnitude of an organism.",,,FALSE,http://purl.obolibrary.org/obo/VT_0100005,assay,,,,Body_Size_Trait_Measurement,Class,Assay,Assay,Imaging_Assay,,, twin spot assay,"Two individual and genetically different populations of cells that originate from the same mitotic recombination event; twin spots allow a direct and reliable comparison between mutant and wild-type clones, and the size of the wild-type twin can serve as a reference for comparison with the homozygous mutant clones.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/29378809/,assay,,,,Twin_Spot_Assay,Class,Assay,Assay,Imaging_Assay,,, perineurial cell thickness,"Measuring the thickness of the cells in the perineurium, e.g. in developing Drosophila melanogaster.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,Perineurial_Cell_Thickness,Class,Assay,Assay,Imaging_Assay,,, -survival,"Any quantitative measurement of survival of or in an individual or study population.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,Perineurial_Cell_Thickness,Class,Assay,Assay,Imaging_Assay,,, +survival,"Any quantitative measurement of survival of or in an individual or study population.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,Perineurial_Cell_Thickness,Class,Assay,Assay,Assay,,, +gait measurement,"Quantification of some aspect of a person's gait such as rhythm, variability or step length",,,FALSE,http://www.ebi.ac.uk/efo/EFO_0007680,assay,,,,Gait_Measurement,Class,Assay,Assay,Physiology_Assay,,, +sorbitol dehydrogenase activity level assay,"An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0003434,assay,,,,Sorbitol_Dehydrogenase_Activity_Level_Assay,Class,Assay,Assay,Cell_Assay,,, +T cell receptor repertoire sequencing,"A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002990,assay,,,,T_Cell_Receptor_Repertoire_Sequencing,Class,Assay,Assay,DNA_Assay,,, +cell proliferation,"A cellular assay that allows for the measurement of the multiplication or reproduction of cells, resulting in the expansion of a cell population.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0000636,assay,,,,Cell_Proliferation,Class,Assay,Assay,Cell_Assay,,, +oxygen consumption assay,"Assay measuring oxygen consumption rate (OCR) to assess changes in metabolism in e.g. cancer cells",,,FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275291/,assay,,,,Oxygen_Consumption_Assay,Class,Assay,Assay,Cell_Assay,,, +reactive oxygen species assay,"Reactive oxygen species (ROS) are measured to assess oxidative events and to investigate their biological importance using antioxidants or inhibitors to modulate the phenomena observed.",,,FALSE,https://www.nature.com/articles/s42255-022-00591-z,assay,,,,Reactive_Oxygen_Species_Assay,Class,Assay,Assay,Cell_Assay,,,See also https://www.nature.com/articles/s42255-022-00591-z for good discussion +ATPase activity assay,"As an assay used for drug discovery, measures enzymatic ATP hydrolysis to help assess levels of enzymatic activity induced by a candidate drug molecule.",,,FALSE,http://purl.obolibrary.org/obo/MI_0880,assay,,,,ATPase_Activity_Assay,Class,Assay,Assay,Cell_Assay,,,See also https://www.bellbrooklabs.com/atpase-activity-assay-for-drug-discovery/ for discussion +novelty response behavior assay,"A behavioral assay devised to measure novelty response behavior",,,FALSE,,assay,,,,Novelty_Response_Behavior_Assay,Class,Assay,Assay,Behavioral_Assay,,, +contextual conditioning behavior assay,"A behavioral assay devised to measure contextual conditioning behavior",,,FALSE,,assay,,,,Contextual_Conditioning_Behavior_Assay,Class,Assay,Assay,Behavioral_Assay,,, +active avoidance learning behavior assay,"A behavioral assay devised to measure active avoidance learning behavior",,,FALSE,,assay,,,,Active_Avoidance_Learning Behavior_Assay,Class,Assay,Assay,Behavioral_Assay,,, +focus forming assay,"The focus forming assay (FFA) is an immunostaining technique and a variation of the viral plaque assay. Instead of detecting the plaque formation after virus-induced cell lysis these assays detect infected host cells and infectious virus particles before a plaque is formed.",,,FALSE,,assay,,,,Focus_Forming_Assay,Class,Assay,Assay,Viral_Assay,,,See https://www.bpes.co.uk/focus-forming-assay-virus-titer-quantitation/ channel,Fluorescent color labeling for an array,"Cy5, Cy3","",TRUE,"",array,,"","",Channel,"",Assay,Assay_Parameter,"","","","" photograph,An image recorded by a camera.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C86035,assay,,"","",Photograph,"",Assay,Assay_Parameter,"","","","" MRISequence,The scanning sequence/modality that is used for a conventional MRI scan.,"T1-weighted,T2-weighted,PD-weighted,Short Tau Inversion Recovery","",FALSE,Sage Bionetworks,experimentalData,,"","",MRI_Sequence,Class,Assay,Assay_Parameter,"","","","" @@ -218,7 +230,7 @@ LifeViz Infinity System,"(From vendor) All-in-one 3D imaging system for face, bo Promega GloMax Discover,"(From vendor) Microplate reader with high-performance luminescence, fluorescence, UV-Visible absorbance, BRET and FRET, two-color filtered luminescence and kinetic measurement capabilities.",,,FALSE,https://www.promega.com/products/microplate-readers-fluorometers-luminometers/microplate-readers/glomax-discover-system/?catNum=GM3000,platform,,,,Promega_GloMax_Discover,Class,Assay,Platform,Platform,,, BGISEQ-500,"(From vendor) BGISEQ-500 is an industry leading high-throughput sequencing solution, powered by combinatorial Probe-Anchor Synthesis (cPAS) and improved DNA Nanoballs (DNB™) technology.",,,FALSE,https://www.bgi.com/wp-content/uploads/sites/4/2017/05/GLOBAL_BGISEQ-500_WholeGenomeSeq_ServiceOverview_04-17.pdf,platform,,,,BGISEQ_500,Assay,Platform,Platform,,, drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,,,drugScreenType,Property,Assay,annotationProperty,,,, -assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography,CUT&RUN,High Frequency Ultrasound, 3D Imaging,Dynamic Light Scattering,Static Light Scattering,flow cytometry,Pattern electroretinogram,Optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy,cell competition,body size trait measurement,twin spot assay,perineurial cell thickness,survival,Phase-Contrast Microscopy",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, +assay,The technology used to generate the data in this file,"HPLC,elevated plus maze test,open field test,rotarod performance test,mRNA counts,high content screen,immunocytochemistry,immunofluorescence,autoradiography,reporter gene assay,electrochemiluminescence,real-time PCR,in vivo tumor growth,blood chemistry measurement,in vivo bioluminescence,immunohistochemistry,NOMe-seq,FIA-MSMS,ultra high-performance liquid chromatography/tandem mass spectrometry,high-performance liquid chromatography/tandem mass spectrometry,liquid chromatography-electrochemical detection,RNA-seq,miRNA-seq,liquid chromatography/tandem mass spectrometry,liquid chromatography/mass spectrometry,lncRNA-seq,whole exome sequencing,Sanger sequencing,ChIP-seq,RNA array,SNP array,methylation array,miRNA array,bisulfite sequencing,ATAC-seq,HI-C,ERR bisulfite sequencing,ISO-seq,western blot,whole genome sequencing,polymerase chain reaction,cell viability assay,2D Incucyte,2D CellTiter-Glo,3D microtissue viability,2D AlamarBlue fluorescence,2D AlamarBlue absorbance,in vivo PDX viability,atomic force microscopy,brightfield microscopy,traction force microscopy,phase-contrast microscopy,next generation targeted sequencing,MIB/MS,scCGI-seq,MudPIT,questionnaire,DNA optical mapping,oxBS-seq,ribo-seq,positron emission tomography,RPPA,ELISA,long term potentiation assay,local field potential recording,whole-cell patch clamp,sandwich ELISA,laser speckle imaging,genotyping,TMT quantitation,mass spectrometry,label free mass spectrometry,cell count,immunoassay,conventional MRI,functional MRI,magnetic resonance spectroscopy,FTIR spectroscopy,rheometry,gel filtration chromatography,differential scanning calorimetry,single molecule drug screen assay,small molecule library screen,combination library screen,combination screen,compound screen,array,single-cell RNA-seq,spatial transcriptomics,massively parallel reporter assay,Riccardi and Ablon scales,spatial frequency domain imaging,optical coherence tomography,CUT&RUN,3D imaging,high frequency ultrasound,dynamic light scattering,static light scattering,light scattering assay,flow cytometry,pattern electroretinogram,optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy,cell competition,body size trait measurement,twin spot assay,perineurial cell thickness,survival,gait measurement,sorbitol dehydrogenase activity level assay,T cell receptor repertoire sequencing,cell proliferation,oxygen consumption assay,reactive oxygen species assay,ATPase activity assay,novelty response behavior assay,contextual conditioning behavior assay,active avoidance learning behavior assay,focus forming assay",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","Illumina HiSeq 3000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina NextSeq 500, Illumina HiSeq 2000, Illumina MiSeq, Zeiss LSM 980, Affymetrix Genome-Wide Human SNP 5.0 Array, Affymetrix Genome-Wide Human SNP 6.0 Array, PacBio RS II, Illumina Genome Analyzer IIx, Illumina HumanOmni1-Quadv1.0, Illumina 1M, Illumina h650, Illumina Omni2pt5M, Illumina Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen 300Karray, Agilent 44Karray, Illumina WholeGenome DASL, Illumina HumanHap300, Nanostring Counter, LTQ Orbitrap XL, Illumina HumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, Affymetrix U133AB, Affymetrix Human Gene 1.0 ST Array, Affymetrix Human Genome U133 Plus 2.0 Array, Illumina HiSeq X, Bionano Irys, Infinium HumanOmniExpressExome, Illumina NextSeq 550, Illumina NextSeq 1000, Illumina NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, Nanostring GeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression,Cherry Imaging TRACE Platform,Cherry Imaging FACE Platform,LifeViz Micro System,LifeViz Infinity System,BGISEQ-500",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, targetCaptureKitID,"A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.",,,TRUE,http://purl.obolibrary.org/obo/NCIT_C177583,experimentalData,,,,targetCaptureKitID,Property,Assay,annotationProperty,,,,"For WES processing, the target BED used could be provided based on the target capture kit." libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,, @@ -226,7 +238,7 @@ assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,F proteinExtractSource,Source of the extracted protein used in the experiment,"cell lysate, nuclei, mitochondria, cytoplasm",,TRUE,http://purl.obolibrary.org/obo/OBI_0000894,experimentalData,,,,proteinExtractSource,Property,Assay,annotationProperty,,,, reporterGene,"A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.",,,FALSE,,experimentalData,,,,reporterGene,Property,Assay,annotationProperty,,,, reporterSubstance,A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.,,,FALSE,,experimentalData,,,,reporterSubstance,Property,Assay,annotationProperty,,,, -immunoAssayType,Type of immuno assay,"ChIPseq, ATAC-seq",,TRUE,,immunoAssay,,,,immunoAssayType,Property,Assay,annotationProperty,,,, +immunoAssayType,Type of immuno assay,"ChIP-seq, ATAC-seq",,TRUE,,immunoAssay,,,,immunoAssayType,Property,Assay,annotationProperty,,,, runType,Is the sequencing run single or paired end?,"singleEnd, pairedEnd","readPair,isStranded,readPairOrientation,readStrandOrigin,readLength,readDepth",FALSE,Sage Bionetworks,ngs,,,,runType,Property,Assay,annotationProperty,ngsParameter,Run_Type,, readPair,The read of origin,,,FALSE,,ngs,,,int,readPair,Property,Assay,annotationProperty,ngsParameter,Read_Pair,, isStranded,Whether or not the library is stranded (Yes; No),"Yes, No",,FALSE,,ngs,,,,isStranded,Property,Assay,annotationProperty,ngsParameter,,, diff --git a/NF.jsonld b/NF.jsonld index eea35b29..6b9f7b50 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -2053,7 +2053,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "mRNAcounts", + "sms:displayName": "mRNA counts", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2087,7 +2087,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Immunocytochemistry", + "sms:displayName": "immunocytochemistry", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2160,10 +2160,10 @@ "sms:validationRules": [] }, { - "@id": "bts:RealTimePCR", + "@id": "bts:Real-timePCR", "@type": "rdfs:Class", "rdfs:comment": "An application of PCR that measures the products generated during each cycle of the polymerase chain reaction process in order to determine the starting amount of template in the reaction.", - "rdfs:label": "RealTimePCR", + "rdfs:label": "Real-timePCR", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2172,7 +2172,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Real Time PCR", + "sms:displayName": "real-time PCR", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2194,10 +2194,10 @@ "sms:validationRules": [] }, { - "@id": "bts:BloodChemistryMeasurement", + "@id": "bts:Bloodchemistrymeasurement", "@type": "rdfs:Class", "rdfs:comment": "The determination of the measured concentrations of chemical constituents of the blood by assay in a clinical laboratory.", - "rdfs:label": "BloodChemistryMeasurement", + "rdfs:label": "Bloodchemistrymeasurement", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2206,7 +2206,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Blood Chemistry Measurement", + "sms:displayName": "blood chemistry measurement", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2245,10 +2245,10 @@ "sms:validationRules": [] }, { - "@id": "bts:NOMe-Seq", + "@id": "bts:NOMe-seq", "@type": "rdfs:Class", "rdfs:comment": "Nucleosome Occupancy and Methylome Sequencing", - "rdfs:label": "NOMe-Seq", + "rdfs:label": "NOMe-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2257,7 +2257,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "NOMe-Seq", + "sms:displayName": "NOMe-seq", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2279,10 +2279,10 @@ "sms:validationRules": [] }, { - "@id": "bts:UPLC-MSMS", + "@id": "bts:Ultrahigh-performanceliquidchromatography/tandemmassspectrometry", "@type": "rdfs:Class", - "rdfs:comment": "Ultra performance liquid chromatography - tandem mass spectrometer.", - "rdfs:label": "UPLC-MSMS", + "rdfs:comment": "UPLC-MSMS is an analytical technique wherein ultra-high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.", + "rdfs:label": "Ultrahigh-performanceliquidchromatography/tandemmassspectrometry", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2291,15 +2291,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "UPLC-MSMS", + "sms:displayName": "ultra high-performance liquid chromatography/tandem mass spectrometry", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:HPLC-MSMS", + "@id": "bts:High-performanceliquidchromatography/tandemmassspectrometry", "@type": "rdfs:Class", - "rdfs:comment": "An analytical technique wherein high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.", - "rdfs:label": "HPLC-MSMS", + "rdfs:comment": "HPLC-MSMS is an analytical technique wherein high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.", + "rdfs:label": "High-performanceliquidchromatography/tandemmassspectrometry", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2308,7 +2308,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "HPLC-MSMS", + "sms:displayName": "high-performance liquid chromatography/tandem mass spectrometry", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2330,10 +2330,10 @@ "sms:validationRules": [] }, { - "@id": "bts:RnaSeq", + "@id": "bts:RNA-seq", "@type": "rdfs:Class", "rdfs:comment": "RNA Sequencing measurements", - "rdfs:label": "RnaSeq", + "rdfs:label": "RNA-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2342,15 +2342,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "rnaSeq", + "sms:displayName": "RNA-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MirnaSeq", + "@id": "bts:MiRNA-seq", "@type": "rdfs:Class", - "rdfs:comment": "Small RNA measurements collected from RNA-Seq experiments", - "rdfs:label": "MirnaSeq", + "rdfs:comment": "Small RNA measurements collected from RNA sequencing experiments", + "rdfs:label": "MiRNA-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2359,15 +2359,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "mirnaSeq", + "sms:displayName": "miRNA-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LC-MSMS", + "@id": "bts:Liquidchromatography/tandemmassspectrometry", "@type": "rdfs:Class", - "rdfs:comment": "A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series", - "rdfs:label": "LC-MSMS", + "rdfs:comment": "LC-MSMS is an analytical technique wherein liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.", + "rdfs:label": "Liquidchromatography/tandemmassspectrometry", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2376,15 +2376,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC-MSMS", + "sms:displayName": "liquid chromatography/tandem mass spectrometry", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LC-MS", + "@id": "bts:Liquidchromatography/massspectrometry", "@type": "rdfs:Class", - "rdfs:comment": "A method where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterised by their mass-to-charge ratio and relative abundance", - "rdfs:label": "LC-MS", + "rdfs:comment": "LC-MS is a hyphenated technique, combining the separation power of liquid chromatography (LC), an analytical chromatographic technique for separating ions or molecules dissolved in a solvent, with the detection power of mass spectrometry(MS), a technique to separate gas phase ions according their m/z (mass to charge ratio) value. Used for drug screening, pharmacology studies, environmental analyses and forensics.", + "rdfs:label": "Liquidchromatography/massspectrometry", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2393,15 +2393,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LC-MS", + "sms:displayName": "liquid chromatography/mass spectrometry", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LncrnaSeq", + "@id": "bts:LncRNA-seq", "@type": "rdfs:Class", "rdfs:comment": "Long non-coding RNA measurements collected from RNA-Seq experiments", - "rdfs:label": "LncrnaSeq", + "rdfs:label": "LncRNA-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2410,15 +2410,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "lncrnaSeq", + "sms:displayName": "lncRNA-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WholeExomeSequencing", + "@id": "bts:Wholeexomesequencing", "@type": "rdfs:Class", "rdfs:comment": "A procedure that can determine the DNA sequence for all of the exons in an individual.", - "rdfs:label": "WholeExomeSequencing", + "rdfs:label": "Wholeexomesequencing", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2427,7 +2427,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Whole Exome Sequencing", + "sms:displayName": "whole exome sequencing", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2449,10 +2449,10 @@ "sms:validationRules": [] }, { - "@id": "bts:ChIPSeq", + "@id": "bts:ChIP-seq", "@type": "rdfs:Class", "rdfs:comment": "Chromatin immuno-precipitation followed by sequencing", - "rdfs:label": "ChIPSeq", + "rdfs:label": "ChIP-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2461,15 +2461,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ChIPSeq", + "sms:displayName": "ChIP-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:RnaArray", + "@id": "bts:RNAarray", "@type": "rdfs:Class", "rdfs:comment": "RNA measurements captured by array technology", - "rdfs:label": "RnaArray", + "rdfs:label": "RNAarray", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2478,15 +2478,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "rnaArray", + "sms:displayName": "RNA array", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SnpArray", + "@id": "bts:SNParray", "@type": "rdfs:Class", "rdfs:comment": "SNP measurements captured by array technology", - "rdfs:label": "SnpArray", + "rdfs:label": "SNParray", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2495,15 +2495,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "snpArray", + "sms:displayName": "SNP array", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MethylationArray", + "@id": "bts:Methylationarray", "@type": "rdfs:Class", "rdfs:comment": "Methylation data captured by array technology", - "rdfs:label": "MethylationArray", + "rdfs:label": "Methylationarray", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2512,15 +2512,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "methylationArray", + "sms:displayName": "methylation array", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MirnaArray", + "@id": "bts:MiRNAarray", "@type": "rdfs:Class", "rdfs:comment": "microRNA measurements captured by array technology", - "rdfs:label": "MirnaArray", + "rdfs:label": "MiRNAarray", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2529,15 +2529,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "mirnaArray", + "sms:displayName": "miRNA array", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BisulfiteSeq", + "@id": "bts:Bisulfitesequencing", "@type": "rdfs:Class", "rdfs:comment": "Methylation data captured by sequencing of DNA treated by a bisulfite-based chemical process", - "rdfs:label": "BisulfiteSeq", + "rdfs:label": "Bisulfitesequencing", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2546,15 +2546,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "bisulfiteSeq", + "sms:displayName": "bisulfite sequencing", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ATACSeq", + "@id": "bts:ATAC-seq", "@type": "rdfs:Class", "rdfs:comment": "Open chromatin regions measured by sequencing DNA after assay for transposase-accessible chromatin (ATAC) treatment", - "rdfs:label": "ATACSeq", + "rdfs:label": "ATAC-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2563,7 +2563,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ATACSeq", + "sms:displayName": "ATAC-seq", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2585,10 +2585,10 @@ "sms:validationRules": [] }, { - "@id": "bts:ErrBisulfiteSeq", + "@id": "bts:ERRbisulfitesequencing", "@type": "rdfs:Class", - "rdfs:comment": "Data for enriched reduced representation bisulfite sequencing data", - "rdfs:label": "ErrBisulfiteSeq", + "rdfs:comment": "Enhanced reduced representation bisulfite sequencing (ERRBS) ", + "rdfs:label": "ERRbisulfitesequencing", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2597,15 +2597,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "errBisulfiteSeq", + "sms:displayName": "ERR bisulfite sequencing", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ISOSeq", + "@id": "bts:ISO-seq", "@type": "rdfs:Class", "rdfs:comment": "Full isoform sequencing", - "rdfs:label": "ISOSeq", + "rdfs:label": "ISO-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2614,15 +2614,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ISOSeq", + "sms:displayName": "ISO-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WesternBlot", + "@id": "bts:Westernblot", "@type": "rdfs:Class", "rdfs:comment": "A multistep process in which a mixture of proteins is separated by gel electrophoresis", - "rdfs:label": "WesternBlot", + "rdfs:label": "Westernblot", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2631,15 +2631,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "westernBlot", + "sms:displayName": "western blot", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:WholeGenomeSeq", + "@id": "bts:Wholegenomesequencing", "@type": "rdfs:Class", "rdfs:comment": "Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time", - "rdfs:label": "WholeGenomeSeq", + "rdfs:label": "Wholegenomesequencing", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2648,15 +2648,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "wholeGenomeSeq", + "sms:displayName": "whole genome sequencing", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PolymeraseChainReaction", + "@id": "bts:Polymerasechainreaction", "@type": "rdfs:Class", "rdfs:comment": "A rapid technique for in vitro amplification of specific DNA or RNA sequences, allowing small quantities of short sequences to be analyzed without cloning", - "rdfs:label": "PolymeraseChainReaction", + "rdfs:label": "Polymerasechainreaction", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2665,15 +2665,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "polymeraseChainReaction", + "sms:displayName": "polymerase chain reaction", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CellViabilityAssay", + "@id": "bts:Cellviabilityassay", "@type": "rdfs:Class", "rdfs:comment": "This assay type measures the cellular state of living or dying by measuring an indicator of life or death", - "rdfs:label": "CellViabilityAssay", + "rdfs:label": "Cellviabilityassay", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2682,7 +2682,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "cellViabilityAssay", + "sms:displayName": "cell viability assay", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2789,10 +2789,10 @@ "sms:validationRules": [] }, { - "@id": "bts:AtomicForceMicroscopy", + "@id": "bts:Atomicforcemicroscopy", "@type": "rdfs:Class", "rdfs:comment": "Microscopy which uses a sharp spike (known as a 'tip') mounted on the end of a cantilever to scan the surface of the specimen", - "rdfs:label": "AtomicForceMicroscopy", + "rdfs:label": "Atomicforcemicroscopy", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2801,15 +2801,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "atomicForceMicroscopy", + "sms:displayName": "atomic force microscopy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:BrightfieldMicroscopy", + "@id": "bts:Brightfieldmicroscopy", "@type": "rdfs:Class", "rdfs:comment": "Microscopy where the specimen is illuminated with light transmitted from a source on the opposite side of the specimen from the objective", - "rdfs:label": "BrightfieldMicroscopy", + "rdfs:label": "Brightfieldmicroscopy", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2818,15 +2818,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "brightfieldMicroscopy", + "sms:displayName": "brightfield microscopy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:TractionForceMicroscopy", + "@id": "bts:Tractionforcemicroscopy", "@type": "rdfs:Class", "rdfs:comment": "An experimental method for determining the tractions on the surface of a biological cell by obtaining measurements of the surrounding displacement field within an in vitro extracellular matrix (ECM)", - "rdfs:label": "TractionForceMicroscopy", + "rdfs:label": "Tractionforcemicroscopy", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2835,15 +2835,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "tractionForceMicroscopy", + "sms:displayName": "traction force microscopy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Phase-ContrastMicroscopy", + "@id": "bts:Phase-contrastmicroscopy", "@type": "rdfs:Class", "rdfs:comment": "A simple non-quantitative form of interference microscopy of great utility in visualising live cells. Small differences in optical path length due to differences in refractive index and thickness of structures are visualised as differences in light intensity.", - "rdfs:label": "Phase-ContrastMicroscopy", + "rdfs:label": "Phase-contrastmicroscopy", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2852,15 +2852,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Phase-Contrast Microscopy", + "sms:displayName": "phase-contrast microscopy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:NextGenerationTargetedSequencing", + "@id": "bts:Nextgenerationtargetedsequencing", "@type": "rdfs:Class", "rdfs:comment": "A type of next generation sequencing in which specific genes or portions of genes are targeted for sequencing using amplicon-based workflow.", - "rdfs:label": "NextGenerationTargetedSequencing", + "rdfs:label": "Nextgenerationtargetedsequencing", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2869,7 +2869,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nextGenerationTargetedSequencing", + "sms:displayName": "next generation targeted sequencing", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2891,10 +2891,10 @@ "sms:validationRules": [] }, { - "@id": "bts:ScCGIseq", + "@id": "bts:ScCGI-seq", "@type": "rdfs:Class", "rdfs:comment": "A method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs", - "rdfs:label": "ScCGIseq", + "rdfs:label": "ScCGI-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2903,7 +2903,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "scCGIseq", + "sms:displayName": "scCGI-seq", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -2959,10 +2959,10 @@ "sms:validationRules": [] }, { - "@id": "bts:OxBS-Seq", + "@id": "bts:OxBS-seq", "@type": "rdfs:Class", "rdfs:comment": "Oxidative bisulfite sequencing (oxBS-Seq) to map 5-methylcytosine and 5-hydroxymethylcytosine", - "rdfs:label": "OxBS-Seq", + "rdfs:label": "OxBS-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2971,15 +2971,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "oxBS-Seq", + "sms:displayName": "oxBS-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:Ribo-Seq", + "@id": "bts:Ribo-seq", "@type": "rdfs:Class", "rdfs:comment": "Ribosome profiling (Ribo-Seq).", - "rdfs:label": "Ribo-Seq", + "rdfs:label": "Ribo-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -2988,15 +2988,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Ribo-Seq", + "sms:displayName": "ribo-seq", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:PositronEmissionTomography", + "@id": "bts:Positronemissiontomography", "@type": "rdfs:Class", "rdfs:comment": "A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue.", - "rdfs:label": "PositronEmissionTomography", + "rdfs:label": "Positronemissiontomography", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3005,7 +3005,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Positron Emission Tomography", + "sms:displayName": "positron emission tomography", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3044,10 +3044,10 @@ "sms:validationRules": [] }, { - "@id": "bts:LTP", + "@id": "bts:Longtermpotentiationassay", "@type": "rdfs:Class", - "rdfs:comment": "Any measurable or observable characteristic related to the persistent robust synaptic response induced by synchronous stimulation of pre- and postsynaptic cells.", - "rdfs:label": "LTP", + "rdfs:comment": "A measure of the persistent robust synaptic response induced by synchronous stimulation of pre- and postsynaptic cells.", + "rdfs:label": "Longtermpotentiationassay", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3056,15 +3056,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LTP", + "sms:displayName": "long term potentiation assay", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:LFP", + "@id": "bts:Localfieldpotentialrecording", "@type": "rdfs:Class", "rdfs:comment": "An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue.", - "rdfs:label": "LFP", + "rdfs:label": "Localfieldpotentialrecording", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3073,7 +3073,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "LFP", + "sms:displayName": "local field potential recording", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3112,10 +3112,10 @@ "sms:validationRules": [] }, { - "@id": "bts:LaserSpeckleImaging", + "@id": "bts:Laserspeckleimaging", "@type": "rdfs:Class", "rdfs:comment": "A noninvasive, non-scanning optical imaging technique that provides full-field visualization of blood flow to the tissue being imaged, which provides information about tissue perfusion and the efficiency of disease treatment.", - "rdfs:label": "LaserSpeckleImaging", + "rdfs:label": "Laserspeckleimaging", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3124,7 +3124,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Laser Speckle Imaging", + "sms:displayName": "laser speckle imaging", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3141,7 +3141,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Genotyping", + "sms:displayName": "genotyping", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3162,6 +3162,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Massspectrometry", + "@type": "rdfs:Class", + "rdfs:comment": "A generic mass spectrometry assay that allows identification and amount of peptide or protein materials.", + "rdfs:label": "Massspectrometry", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "mass spectrometry", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Labelfreemassspectrometry", "@type": "rdfs:Class", @@ -3197,10 +3214,10 @@ "sms:validationRules": [] }, { - "@id": "bts:ImmunoAssay", + "@id": "bts:Immunoassay", "@type": "rdfs:Class", "rdfs:comment": "Generic immunology assay", - "rdfs:label": "ImmunoAssay", + "rdfs:label": "Immunoassay", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3209,7 +3226,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "immunoAssay", + "sms:displayName": "immunoassay", "sms:required": "sms:false", "sms:requiresDependency": [ { @@ -3231,7 +3248,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Conventional MRI", + "sms:displayName": "conventional MRI", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3248,15 +3265,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Functional MRI", + "sms:displayName": "functional MRI", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:MagneticResonanceSpectroscopy", + "@id": "bts:Magneticresonancespectroscopy", "@type": "rdfs:Class", "rdfs:comment": "Detection and measurement of the resonant spectra of molecular species in a tissue or sample.", - "rdfs:label": "MagneticResonanceSpectroscopy", + "rdfs:label": "Magneticresonancespectroscopy", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3265,15 +3282,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Magnetic Resonance Spectroscopy", + "sms:displayName": "magnetic resonance spectroscopy", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:FTIRSpectroscopy", + "@id": "bts:FTIRspectroscopy", "@type": "rdfs:Class", "rdfs:comment": "Fourier transform infrared (FTIR) spectroscopy is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid or gas. An FTIR spectrometer simultaneously collects high-resolution spectral data over a wide spectral range.", - "rdfs:label": "FTIRSpectroscopy", + "rdfs:label": "FTIRspectroscopy", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3282,7 +3299,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "FTIR Spectroscopy", + "sms:displayName": "FTIR spectroscopy", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3316,7 +3333,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Gel filtration chromatography", + "sms:displayName": "gel filtration chromatography", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3338,10 +3355,10 @@ "sms:validationRules": [] }, { - "@id": "bts:SingleMolecule", + "@id": "bts:Singlemoleculedrugscreenassay", "@type": "rdfs:Class", "rdfs:comment": "An experiment in which a single molecule was used in an assay", - "rdfs:label": "SingleMolecule", + "rdfs:label": "Singlemoleculedrugscreenassay", "rdfs:subClassOf": [ { "@id": "bts:DrugScreenType" @@ -3350,15 +3367,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "singleMolecule", + "sms:displayName": "single molecule drug screen assay", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:SmallMoleculeLibraryScreen", + "@id": "bts:Smallmoleculelibraryscreen", "@type": "rdfs:Class", "rdfs:comment": "High throughput sample analysis of small molecules for purpose such as drug discovery, or biochemical, genetic or pharmacological tests.", - "rdfs:label": "SmallMoleculeLibraryScreen", + "rdfs:label": "Smallmoleculelibraryscreen", "rdfs:subClassOf": [ { "@id": "bts:DrugScreenType" @@ -3367,15 +3384,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "smallMoleculeLibraryScreen", + "sms:displayName": "small molecule library screen", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CombinationLibraryScreen", + "@id": "bts:Combinationlibraryscreen", "@type": "rdfs:Class", "rdfs:comment": "High throughput sample analysis of collections of compounds that provide a variety of chemically diverse structures that can be used to identify structure types that have affinity with pharmacological targets.", - "rdfs:label": "CombinationLibraryScreen", + "rdfs:label": "Combinationlibraryscreen", "rdfs:subClassOf": [ { "@id": "bts:DrugScreenType" @@ -3384,15 +3401,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "combinationLibraryScreen", + "sms:displayName": "combination library screen", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CombinationScreen", + "@id": "bts:Combinationscreen", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "CombinationScreen", + "rdfs:label": "Combinationscreen", "rdfs:subClassOf": [ { "@id": "bts:DrugScreenType" @@ -3401,15 +3418,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "combinationScreen", + "sms:displayName": "combination screen", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:CompoundScreen", + "@id": "bts:Compoundscreen", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "CompoundScreen", + "rdfs:label": "Compoundscreen", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3418,7 +3435,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "compoundScreen", + "sms:displayName": "compound screen", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3440,10 +3457,10 @@ "sms:validationRules": [] }, { - "@id": "bts:SingleCellRNASequencing", + "@id": "bts:Single-cellRNA-seq", "@type": "rdfs:Class", "rdfs:comment": "A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.", - "rdfs:label": "SingleCellRNASequencing", + "rdfs:label": "Single-cellRNA-seq", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3452,7 +3469,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Single Cell RNA Sequencing", + "sms:displayName": "single-cell RNA-seq", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3474,10 +3491,10 @@ "sms:validationRules": [] }, { - "@id": "bts:MassivelyParallelReporterAssay", + "@id": "bts:Massivelyparallelreporterassay", "@type": "rdfs:Class", "rdfs:comment": "An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.", - "rdfs:label": "MassivelyParallelReporterAssay", + "rdfs:label": "Massivelyparallelreporterassay", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3486,7 +3503,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Massively Parallel Reporter Assay", + "sms:displayName": "massively parallel reporter assay", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3508,10 +3525,10 @@ "sms:validationRules": [] }, { - "@id": "bts:SpatialFrequencyDomainImaging", + "@id": "bts:Spatialfrequencydomainimaging", "@type": "rdfs:Class", "rdfs:comment": "Spatial Frequency Domain Imaging (SFDI) is a non-contact, depth-varying and wide-field optical imaging technique for measuring optical properties in a wide field-of-view on a pixel-by-pixel basis. Relevant applications include including burn assessment, skin tissue evaluation, tumor tissue detection, brain tissue monitoring.", - "rdfs:label": "SpatialFrequencyDomainImaging", + "rdfs:label": "Spatialfrequencydomainimaging", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3520,15 +3537,15 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Spatial Frequency Domain Imaging", + "sms:displayName": "spatial frequency domain imaging", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:OpticalCoherenceTomography", + "@id": "bts:Opticalcoherencetomography", "@type": "rdfs:Class", "rdfs:comment": "Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition", - "rdfs:label": "OpticalCoherenceTomography", + "rdfs:label": "Opticalcoherencetomography", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3537,7 +3554,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Optical Coherence Tomography", + "sms:displayName": "optical coherence tomography", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3559,10 +3576,10 @@ "sms:validationRules": [] }, { - "@id": "bts:3DImaging", + "@id": "bts:3Dimaging", "@type": "rdfs:Class", "rdfs:comment": "Technique to produce 3D images to visualize important structures in great detail. To produce 3D images, many scans are made, and then combined by computers to produce a 3D model, which can then be manipulated. 3D ultrasounds are produced using a somewhat similar technique.", - "rdfs:label": "3DImaging", + "rdfs:label": "3Dimaging", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3571,7 +3588,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "3D Imaging", + "sms:displayName": "3D imaging", "sms:required": "sms:false", "sms:requiresDependency": [ { @@ -3581,10 +3598,10 @@ "sms:validationRules": [] }, { - "@id": "bts:HighFrequencyUltrasound", + "@id": "bts:Highfrequencyultrasound", "@type": "rdfs:Class", "rdfs:comment": "High frequency ultrasound (HFUS) is an imaging modality that can give greater resolution of surface changes in skin (review in PMID:24583666)", - "rdfs:label": "HighFrequencyUltrasound", + "rdfs:label": "Highfrequencyultrasound", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3593,7 +3610,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "High Frequency Ultrasound", + "sms:displayName": "high frequency ultrasound", "sms:required": "sms:false", "sms:requiresDependency": [ { @@ -3603,10 +3620,10 @@ "sms:validationRules": [] }, { - "@id": "bts:DynamicLightScattering", + "@id": "bts:Dynamiclightscattering", "@type": "rdfs:Class", "rdfs:comment": "Dynamic Light Scattering (DLS), also known as photocorrelation spectroscopy, is a method for determining the size distribution of a sample of small particles in solution by illuminating the sample with a light source (usually a laser) and measuring the time-dependent fluctuations in the intensity of the scattered light caused by Brownian motion.", - "rdfs:label": "DynamicLightScattering", + "rdfs:label": "Dynamiclightscattering", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3615,7 +3632,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Dynamic Light Scattering", + "sms:displayName": "dynamic light scattering", "sms:required": "sms:false", "sms:requiresDependency": [ { @@ -3625,10 +3642,10 @@ "sms:validationRules": [] }, { - "@id": "bts:StaticLightScattering", + "@id": "bts:Staticlightscattering", "@type": "rdfs:Class", "rdfs:comment": "Static Light Scattering is a method for determining structure by measuring the total or time-averaged scattering intensity of scattered visible light as a function of angle.", - "rdfs:label": "StaticLightScattering", + "rdfs:label": "Staticlightscattering", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3637,7 +3654,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Static Light Scattering", + "sms:displayName": "static light scattering", "sms:required": "sms:false", "sms:requiresDependency": [ { @@ -3647,10 +3664,10 @@ "sms:validationRules": [] }, { - "@id": "bts:LightScatteringAssay", + "@id": "bts:Lightscatteringassay", "@type": "rdfs:Class", "rdfs:comment": "A method for determining structure by measuring the change in direction or energy of scattered visible light. Light is scattered by the electrons surrounding the atomic nuclei in the sample.", - "rdfs:label": "LightScatteringAssay", + "rdfs:label": "Lightscatteringassay", "rdfs:subClassOf": [ { "@id": "bts:Assay" @@ -3659,7 +3676,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Light Scattering Assay", + "sms:displayName": "light scattering assay", "sms:required": "sms:false", "sms:requiresDependency": [ { @@ -3698,7 +3715,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Pattern electroretinogram", + "sms:displayName": "pattern electroretinogram", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3715,7 +3732,7 @@ "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "Optokinetic reflex assay", + "sms:displayName": "optokinetic reflex assay", "sms:required": "sms:false", "sms:validationRules": [] }, @@ -3855,6 +3872,193 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Gaitmeasurement", + "@type": "rdfs:Class", + "rdfs:comment": "Quantification of some aspect of a person's gait such as rhythm, variability or step length", + "rdfs:label": "Gaitmeasurement", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "gait measurement", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Sorbitoldehydrogenaseactivitylevelassay", + "@type": "rdfs:Class", + "rdfs:comment": "An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample.", + "rdfs:label": "Sorbitoldehydrogenaseactivitylevelassay", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "sorbitol dehydrogenase activity level assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Tcellreceptorrepertoiresequencing", + "@type": "rdfs:Class", + "rdfs:comment": "A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample.", + "rdfs:label": "Tcellreceptorrepertoiresequencing", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "T cell receptor repertoire sequencing", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Cellproliferation", + "@type": "rdfs:Class", + "rdfs:comment": "A cellular assay that allows for the measurement of the multiplication or reproduction of cells, resulting in the expansion of a cell population.", + "rdfs:label": "Cellproliferation", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "cell proliferation", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Oxygenconsumptionassay", + "@type": "rdfs:Class", + "rdfs:comment": "Assay measuring oxygen consumption rate (OCR) to assess changes in metabolism in e.g. cancer cells", + "rdfs:label": "Oxygenconsumptionassay", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "oxygen consumption assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Reactiveoxygenspeciesassay", + "@type": "rdfs:Class", + "rdfs:comment": "Reactive oxygen species (ROS) are measured to assess oxidative events and to investigate their biological importance using antioxidants or inhibitors to modulate the phenomena observed.", + "rdfs:label": "Reactiveoxygenspeciesassay", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "reactive oxygen species assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:ATPaseactivityassay", + "@type": "rdfs:Class", + "rdfs:comment": "As an assay used for drug discovery, measures enzymatic ATP hydrolysis to help assess levels of enzymatic activity induced by a candidate drug molecule.", + "rdfs:label": "ATPaseactivityassay", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "ATPase activity assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Noveltyresponsebehaviorassay", + "@type": "rdfs:Class", + "rdfs:comment": "A behavioral assay devised to measure novelty response behavior", + "rdfs:label": "Noveltyresponsebehaviorassay", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "novelty response behavior assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Contextualconditioningbehaviorassay", + "@type": "rdfs:Class", + "rdfs:comment": "A behavioral assay devised to measure contextual conditioning behavior", + "rdfs:label": "Contextualconditioningbehaviorassay", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "contextual conditioning behavior assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Activeavoidancelearningbehaviorassay", + "@type": "rdfs:Class", + "rdfs:comment": "A behavioral assay devised to measure active avoidance learning behavior", + "rdfs:label": "Activeavoidancelearningbehaviorassay", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "active avoidance learning behavior assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Focusformingassay", + "@type": "rdfs:Class", + "rdfs:comment": "The focus forming assay (FFA) is an immunostaining technique and a variation of the viral plaque assay. Instead of detecting the plaque formation after virus-induced cell lysis these assays detect infected host cells and infectious virus particles before a plaque is formed.", + "rdfs:label": "Focusformingassay", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "focus forming assay", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Channel", "@type": "rdfs:Class", @@ -5775,6 +5979,9 @@ "@id": "http://schema.biothings.io" }, "schema:rangeIncludes": [ + { + "@id": "bts:HPLC" + }, { "@id": "bts:Elevatedplusmazetest" }, @@ -5800,19 +6007,19 @@ "@id": "bts:Autoradiography" }, { - "@id": "bts:Electrochemiluminescence" + "@id": "bts:Reportergeneassay" }, { - "@id": "bts:RealTimePCR" + "@id": "bts:Electrochemiluminescence" }, { - "@id": "bts:Invivotumorgrowth" + "@id": "bts:Real-timePCR" }, { - "@id": "bts:Scale" + "@id": "bts:Invivotumorgrowth" }, { - "@id": "bts:BloodChemistryMeasurement" + "@id": "bts:Bloodchemistrymeasurement" }, { "@id": "bts:Invivobioluminescence" @@ -5821,103 +6028,121 @@ "@id": "bts:Immunohistochemistry" }, { - "@id": "bts:NOMe-Seq" + "@id": "bts:NOMe-seq" }, { "@id": "bts:FIA-MSMS" }, { - "@id": "bts:UPLC-MSMS" + "@id": "bts:Ultrahigh-performanceliquidchromatography/tandemmassspectrometry" }, { - "@id": "bts:HPLC-MSMS" + "@id": "bts:High-performanceliquidchromatography/tandemmassspectrometry" }, { "@id": "bts:Liquidchromatography-electrochemicaldetection" }, { - "@id": "bts:RnaSeq" + "@id": "bts:RNA-seq" }, { - "@id": "bts:MirnaSeq" + "@id": "bts:MiRNA-seq" }, { - "@id": "bts:LC-MSMS" + "@id": "bts:Liquidchromatography/tandemmassspectrometry" }, { - "@id": "bts:LC-MS" + "@id": "bts:Liquidchromatography/massspectrometry" }, { - "@id": "bts:LncrnaSeq" + "@id": "bts:LncRNA-seq" }, { - "@id": "bts:WholeExomeSequencing" + "@id": "bts:Wholeexomesequencing" }, { "@id": "bts:Sangersequencing" }, { - "@id": "bts:ChIPSeq" + "@id": "bts:ChIP-seq" }, { - "@id": "bts:RnaArray" + "@id": "bts:RNAarray" }, { - "@id": "bts:SnpArray" + "@id": "bts:SNParray" }, { - "@id": "bts:MethylationArray" + "@id": "bts:Methylationarray" }, { - "@id": "bts:MirnaArray" + "@id": "bts:MiRNAarray" }, { - "@id": "bts:BisulfiteSeq" + "@id": "bts:Bisulfitesequencing" }, { - "@id": "bts:ATACSeq" + "@id": "bts:ATAC-seq" }, { "@id": "bts:HI-C" }, { - "@id": "bts:ErrBisulfiteSeq" + "@id": "bts:ERRbisulfitesequencing" }, { - "@id": "bts:ISOSeq" + "@id": "bts:ISO-seq" }, { - "@id": "bts:WesternBlot" + "@id": "bts:Westernblot" }, { - "@id": "bts:WholeGenomeSeq" + "@id": "bts:Wholegenomesequencing" }, { - "@id": "bts:PolymeraseChainReaction" + "@id": "bts:Polymerasechainreaction" }, { - "@id": "bts:CellViabilityAssay" + "@id": "bts:Cellviabilityassay" }, { - "@id": "bts:AtomicForceMicroscopy" + "@id": "bts:2DIncucyte" }, { - "@id": "bts:BrightfieldMicroscopy" + "@id": "bts:2DCellTiter-Glo" }, { - "@id": "bts:TractionForceMicroscopy" + "@id": "bts:3Dmicrotissueviability" }, { - "@id": "bts:NextGenerationTargetedSequencing" + "@id": "bts:2DAlamarBluefluorescence" }, { - "@id": "bts:JumpingLibrary" + "@id": "bts:2DAlamarBlueabsorbance" + }, + { + "@id": "bts:InvivoPDXviability" + }, + { + "@id": "bts:Atomicforcemicroscopy" + }, + { + "@id": "bts:Brightfieldmicroscopy" + }, + { + "@id": "bts:Tractionforcemicroscopy" + }, + { + "@id": "bts:Phase-contrastmicroscopy" + }, + { + "@id": "bts:Nextgenerationtargetedsequencing" }, { "@id": "bts:MIB/MS" }, { - "@id": "bts:ScCGIseq" + "@id": "bts:ScCGI-seq" }, { "@id": "bts:MudPIT" @@ -5929,13 +6154,13 @@ "@id": "bts:DNAopticalmapping" }, { - "@id": "bts:OxBS-Seq" + "@id": "bts:OxBS-seq" }, { - "@id": "bts:Ribo-Seq" + "@id": "bts:Ribo-seq" }, { - "@id": "bts:PositronEmissionTomography" + "@id": "bts:Positronemissiontomography" }, { "@id": "bts:RPPA" @@ -5944,10 +6169,10 @@ "@id": "bts:ELISA" }, { - "@id": "bts:LTP" + "@id": "bts:Longtermpotentiationassay" }, { - "@id": "bts:LFP" + "@id": "bts:Localfieldpotentialrecording" }, { "@id": "bts:Whole-cellpatchclamp" @@ -5956,7 +6181,7 @@ "@id": "bts:SandwichELISA" }, { - "@id": "bts:LaserSpeckleImaging" + "@id": "bts:Laserspeckleimaging" }, { "@id": "bts:Genotyping" @@ -5964,6 +6189,9 @@ { "@id": "bts:TMTquantitation" }, + { + "@id": "bts:Massspectrometry" + }, { "@id": "bts:Labelfreemassspectrometry" }, @@ -5971,79 +6199,82 @@ "@id": "bts:Cellcount" }, { - "@id": "bts:Reportergeneassay" + "@id": "bts:Immunoassay" }, { - "@id": "bts:SingleCellRNASequencing" + "@id": "bts:ConventionalMRI" }, { - "@id": "bts:Spatialtranscriptomics" + "@id": "bts:FunctionalMRI" }, { - "@id": "bts:ConventionalMRI" + "@id": "bts:Magneticresonancespectroscopy" }, { - "@id": "bts:FunctionalMRI" + "@id": "bts:FTIRspectroscopy" }, { - "@id": "bts:MagneticResonanceSpectroscopy" + "@id": "bts:Rheometry" }, { - "@id": "bts:2DIncucyte" + "@id": "bts:Gelfiltrationchromatography" }, { - "@id": "bts:2DCellTiter-Glo" + "@id": "bts:Differentialscanningcalorimetry" }, { - "@id": "bts:3Dmicrotissueviability" + "@id": "bts:Singlemoleculedrugscreenassay" }, { - "@id": "bts:InvivoPDXviability" + "@id": "bts:Smallmoleculelibraryscreen" }, { - "@id": "bts:2DAlamarBluefluorescence" + "@id": "bts:Combinationlibraryscreen" }, { - "@id": "bts:2DAlamarBlueabsorbance" + "@id": "bts:Combinationscreen" }, { - "@id": "bts:Rheometry" + "@id": "bts:Compoundscreen" }, { - "@id": "bts:FTIRSpectroscopy" + "@id": "bts:Array" }, { - "@id": "bts:Differentialscanningcalorimetry" + "@id": "bts:Single-cellRNA-seq" }, { - "@id": "bts:Gelfiltrationchromatography" + "@id": "bts:Spatialtranscriptomics" }, { - "@id": "bts:MassivelyParallelReporterAssay" + "@id": "bts:Massivelyparallelreporterassay" }, { "@id": "bts:RiccardiandAblonscales" }, { - "@id": "bts:SpatialFrequencyDomainImaging" + "@id": "bts:Spatialfrequencydomainimaging" }, { - "@id": "bts:OpticalCoherenceTomography" + "@id": "bts:Opticalcoherencetomography" }, { "@id": "bts:CUT&RUN" }, { - "@id": "bts:HighFrequencyUltrasound" + "@id": "bts:3Dimaging" + }, + { + "@id": "bts:Highfrequencyultrasound" }, { - "@id": "bts:3DImaging" + "@id": "bts:Dynamiclightscattering" }, { - "@id": "bts:DynamicLightScattering" + "@id": "bts:Staticlightscattering" }, { - "@id": "bts:StaticLightScattering" + "@id": "bts:Lightscatteringassay" }, { "@id": "bts:Flowcytometry" @@ -6079,7 +6310,37 @@ "@id": "bts:Survival" }, { - "@id": "bts:Phase-ContrastMicroscopy" + "@id": "bts:Gaitmeasurement" + }, + { + "@id": "bts:Sorbitoldehydrogenaseactivitylevelassay" + }, + { + "@id": "bts:Tcellreceptorrepertoiresequencing" + }, + { + "@id": "bts:Cellproliferation" + }, + { + "@id": "bts:Oxygenconsumptionassay" + }, + { + "@id": "bts:Reactiveoxygenspeciesassay" + }, + { + "@id": "bts:ATPaseactivityassay" + }, + { + "@id": "bts:Noveltyresponsebehaviorassay" + }, + { + "@id": "bts:Contextualconditioningbehaviorassay" + }, + { + "@id": "bts:Activeavoidancelearningbehaviorassay" + }, + { + "@id": "bts:Focusformingassay" } ], "sms:displayName": "assay", @@ -6392,7 +6653,7 @@ }, "schema:rangeIncludes": [ { - "@id": "bts:ChIPseq" + "@id": "bts:ChIP-seq" }, { "@id": "bts:ATAC-seq" @@ -20986,53 +21247,87 @@ "sms:validationRules": [] }, { - "@id": "bts:Nuclei", + "@id": "bts:SingleMolecule", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "Nuclei", + "rdfs:label": "SingleMolecule", "rdfs:subClassOf": [ { - "@id": "bts:ProteinExtractSource" + "@id": "bts:DrugScreenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "nuclei", + "sms:displayName": "singleMolecule", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ChIPseq", + "@id": "bts:SmallMoleculeLibraryScreen", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ChIPseq", + "rdfs:label": "SmallMoleculeLibraryScreen", "rdfs:subClassOf": [ { - "@id": "bts:ImmunoAssayType" + "@id": "bts:DrugScreenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ChIPseq", + "sms:displayName": "smallMoleculeLibraryScreen", "sms:required": "sms:false", "sms:validationRules": [] }, { - "@id": "bts:ATAC-seq", + "@id": "bts:CombinationLibraryScreen", "@type": "rdfs:Class", "rdfs:comment": "TBD", - "rdfs:label": "ATAC-seq", + "rdfs:label": "CombinationLibraryScreen", "rdfs:subClassOf": [ { - "@id": "bts:ImmunoAssayType" + "@id": "bts:DrugScreenType" } ], "schema:isPartOf": { "@id": "http://schema.biothings.io" }, - "sms:displayName": "ATAC-seq", + "sms:displayName": "combinationLibraryScreen", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:CombinationScreen", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "CombinationScreen", + "rdfs:subClassOf": [ + { + "@id": "bts:DrugScreenType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "combinationScreen", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Nuclei", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Nuclei", + "rdfs:subClassOf": [ + { + "@id": "bts:ProteinExtractSource" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "nuclei", "sms:required": "sms:false", "sms:validationRules": [] }, diff --git a/ext_classes.csv b/ext_classes.csv index d64d91b5..bddab73c 100644 --- a/ext_classes.csv +++ b/ext_classes.csv @@ -1,4 +1,5 @@ Attribute,.ID,.Type,.Root,.SubOf +Physiology_Assay,Physiology_Assay,Class,Assay, Experimental_Assay,Assay,Class,Assay, DNA_Assay,DNA_Assay,Class,Assay,Assay RNA_Assay,RNA_Assay,Class,Assay,Assay @@ -10,8 +11,9 @@ Epigenetics_Assay,Epigenetics_Assay,Class,Assay,Assay Imaging_Assay,Imaging_Assay,Class,Assay,Assay Volume_Measurement_Assay,Volume_Measurement_Assay,Class,Assay,Assay Drug_Screen,Drug_Screen,Class,Assay,Assay -Electrophysiology_Assay,Electrophysiology_Assay,Class,Assay,Assay +Electrophysiology_Assay,Electrophysiology_Assay,Class,Assay,Physiology_Assay MRI_Assay,MRI_Assay,Class,Assay,Imaging_Assay +Viral_Assay,MRI_Assay,Class,Assay,Assay Assay_Template,Assay_Template,Class,Template,Manifest_Template Non_Assay_Template,Non_Assay_Template,Class,Template,Template Manifest_Template,Manifest_Template,Class,Template,Template diff --git a/mappings/NFDataPortal/assay_v75.yaml b/mappings/NFDataPortal/assay_v75.yaml new file mode 100644 index 00000000..4ed6905a --- /dev/null +++ b/mappings/NFDataPortal/assay_v75.yaml @@ -0,0 +1,188 @@ +title: Mapping of NF data portal assay concept labels to assay labels in NF data model v6.4 +description: This translates NF data portal assay labels in use around March 2023 (Portal - Files table version 75) to new preferred labels in NF data model v6.4. (Only assay labels being translated are included.) +source_scope: https://www.synapse.org/#!Synapse:syn16858331.75/tables/ +target_scope: hhttps://github.com/nf-osi/nf-metadata-dictionary/releases/tag/v6.4 +mapping: + - source: Whole Exome Sequencing + target: + label: whole exome sequencing + - source: rnaSeq + target: + label: RNA-seq + - source: wholeGenomeSeq + target: + label: whole genome sequencing + - source: Conventional MRI + target: + label: conventional MRI + - source: cellViabilityAssay + target: + label: cell viability assay + - source: westernBlot + target: + label: western blot + - source: brightfieldMicroscopy + target: + label: brightfield microscopy + - source: High Frequency Ultrasound + target: + label: high frequency ultrasound + - source: methylationArray + target: + label: methylation array + - source: nextGenerationTargetedSequencing + target: + label: next generation targeted sequencing + - source: confocalMicroscopy + target: + label: confocal microscopy + - source: 3D Imaging + target: + label: 3D imaging + - source: Positron Emission Tomography + target: + label: positron emission tomography + - source: Immunocytochemistry + target: + label: immunocytochemistry + - source: bisulfiteSeq + target: + label: bisulfite sequencing + - source: snpArray + target: + label: SNP array + - source: single-cell RNAseq + target: + label: single-cell RNA-seq + - source: Single Cell RNA Sequencing + target: + label: single-cell RNA-seq + - source: rnaArray + target: + label: RNA array + - source: Blood Chemistry Measurement + target: + label: blood chemistry measurement + - source: Mass spectrometry + target: + label: mass spectrometry + - source: ATACSeq + target: + label: ATAC-seq + - source: Real Time PCR + target: + label: real-time PCR + - source: jumpingLibrary + target: + label: jumping library + - source: ChIPSeq + target: + label: ChIP-seq + - source: T cell receptor sequencing + target: + label: T cell receptor repertoire sequencing + - source: Microscopy + target: + label: microscopy + - source: SDH enzymatic activity + target: + label: sorbitol dehydrogenase activity level assay + - source: exomeSeq-private + target: + label: whole exome sequencing + - source: polymeraseChainReaction + target: + label: polymerase chain reaction + - source: Focus forming assay + target: + label: focus forming assay + - source: FACS + target: + label: flow cytometry + - source: Flow Cytometry + target: + label: flow cytometry + - source: Immunoassay + target: + label: immunoassay + - source: Cell proliferation + target: + label: cell proliferation assay + - source: Phase-Contrast Microscopy + target: + label: phase-contrast microscopy + - source: atomicForceMicroscopy + target: + label: atomic force microscopy + - source: Cell viability assay + target: + label: cell viability assay + - source: cell counts + target: + label: cell count + - source: drugScreen + target: + label: drug screen + - source: Gel chromatography + target: + label: gel filtration chromatography + - source: novelty response behavior, in vivo bioluminescence + target: + label: novelty response behavior assay + - source: TRAP1 and Hsp90 ATPase activities + target: + label: ATPase activity assay + - source: TRAP1 ATPase activity + target: + label: ATPase activity assay + - source: ATP hydrolisi rate + target: + label: ATPase activity assay + - source: ATP hydrolisis rate + target: + label: ATPase activity assay + - source: contextual conditioning behavior, in vivo bioluminescence + target: + label: contextual conditioning behavior assay + - source: Magnetic Resonance Spectroscopy + target: + label: magnetic resonance spectroscopy + - source: Mass identification + target: + label: mass spectrometry + - source: Measurement of ROS levels + target: + label: reactive oxygen species assay + - source: OCR + target: + label: oxygen consumption assay + - source: Oxigen compustion rate + target: + label: oxygen consumption assay + - source: Oxigen comsuption rate + target: + label: oxygen consumption assay + - source: scale,elevated T maze apparatus method,von Frey,FitBark + target: + label: elevated plus maze test + - source: SDS page + target: + label: SDS-PAGE + - source: wholeGenomeSeq,MudPIT + target: + label: whole genome sequencing + - source: Zeno Electronic Walkway + target: + label: gait measurement +- source: UPLC-MSMS + target: + label: ultra high-performance liquid chromatography/tandem mass spectrometry +- source: HPLC-MSMS + target: + label: high-performance liquid chromatography/tandem mass spectrometry +- source: LC-MSMS + target: + label: liquid chromatography/tandem mass spectrometry +- source: LC-MS + target: + label: liquid chromatography/mass spectrometry diff --git a/mappings/README.md b/mappings/README.md index 17b83d42..8614078e 100644 --- a/mappings/README.md +++ b/mappings/README.md @@ -1,15 +1,19 @@ ## Mappings -This directory stores mapping specifications from the NF data model to other data model/dictionaries as needed in a specific YAML/JSON format. -These mappings are very much in development so both format and content may change. +This directory stores mapping specifications for the NF data model in a specific YAML/JSON format: +1. Translation of NF concepts to *other* data models/dictionaries. +2. Translation of messy or legacy NF Data Portal annotations to versioned, standardized NF data model concepts. + +These mappings help document what was done when metadata are translated or updated in harmonization or migration efforts. +The mappings themselves are in development so both format and content may change. Currently, the map spec is inspired by and vaguely resembles a [concept map](https://build.fhir.org/conceptmap-example.json.html), though [SSOM](https://github.com/mapping-commons/sssom) was also considered. -Mappings may not map from NF to other models in full scope; that is, often we don't map every single data element, only what is needed and applicable given the two models. +Mappings may not map from NF to other models in full scope; that is, often we don't map every single data element, only what is needed and applicable at the time. Additional future mappings that might be useful are: +(To other data models) - NF to [CSBC](https://www.synapse.org/#!Synapse:syn26433610/tables/) - NF to [HTAN](https://github.com/ncihtan/data-models) - NF to [synapseAnnotations](https://github.com/Sage-Bionetworks/synapseAnnotations/) (NF terms originally derived from here, but there has been some drift/divergence) - diff --git a/mappings/cBioPortal.yaml b/mappings/cBioPortal/cBioPortal.yaml similarity index 100% rename from mappings/cBioPortal.yaml rename to mappings/cBioPortal/cBioPortal.yaml diff --git a/modules/Assay/Assay.csv b/modules/Assay/Assay.csv index 8f3d0a8b..0dbf1177 100644 --- a/modules/Assay/Assay.csv +++ b/modules/Assay/Assay.csv @@ -3,103 +3,104 @@ HPLC,"Frequently referred to simply as HPLC, this form of column chromatography elevated plus maze test,"A method which utilizes an experimental apparatus consisting of four arms, usually two enclosed and two open, in the shape of a plus (+) upon which the test animal can walk. The maze is elevated a set distance, for example 40 to 60 centimeters, above the floor or platform upon which the apparatus sits.",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000262,assay,,,,Elevated_Plus_Maze_Test,Class,Assay,Assay,Behavioral_Assay,,, open field test,"A test utilizing an enclosure consisting of a single area bordered by clear or opaque walls, used to measure movement, exploratory behavior, etc of an experimental subject.",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000258,assay,,,,Open_Field_Test,Class,Assay,Assay,Behavioral_Assay,,, rotarod performance test,"A method that utilizes a device consisting of a rotating rod the speed of which is mechanically driven and precisely controlled, for instance held constant or accelerated. The rotarod test is often used to measure riding time or endurance in order to evaluate balance, motor coordination or grip strength.",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000567,assay,,,,Rotarod_Performance_Test,Class,Assay,Assay,Behavioral_Assay,,, -mRNAcounts,A mRNA profiling assay using digital molecular barcoding technology to quantify target mRNA molecules without the need for amplification.,,,FALSE,Sage Bionetworks,assay,,,,MRNA_Counts,Class,Assay,Assay,RNA_Assay,,, +mRNA counts,A mRNA profiling assay using digital molecular barcoding technology to quantify target mRNA molecules without the need for amplification.,,,FALSE,Sage Bionetworks,assay,,,,MRNA_Counts,Class,Assay,Assay,RNA_Assay,,, high content screen,An image analysis technique combining automated fluorescence microscopy with multi-parameter quantitative image analysis for the large scale study of cells (cellomics).,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0007550,assay,,,,High_Content_Screen,Class,Assay,Assay,Imaging_Assay,,, -Immunocytochemistry,The branch of immunochemistry dealing with cells and cellular activity; the application of immunochemical techniques to cytochemistry.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17731,assay,,,,Immunocytochemistry,Class,Assay,Assay,Immuno_Assay,,, +immunocytochemistry,The branch of immunochemistry dealing with cells and cellular activity; the application of immunochemical techniques to cytochemistry.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17731,assay,,,,Immunocytochemistry,Class,Assay,Assay,Immuno_Assay,,, immunofluorescence,An immunological procedure in which the antibodies are coupled with molecules which fluoresce under ultra violet (UV) light. This makes them particularly suitable for detection of specific antigens in tissues or on cells.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17370,assay,,,,Immunofluorescence,Class,Assay,Assay,Immuno_Assay,,, autoradiography,A radioactivity detection technique using X- ray film to visualize molecules or fragments of molecules that have been radioactively labeled.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0000716,assay,,,,Autoradiography,Class,Assay,Assay,Radio_Assay,,, reporter gene assay,"Reporter gene assay measures the gene expression from a reporter gene. The reporter gene is inserted under the control of a foreign promoter or an artificial regulatory element of interest. Reporters include luciferase, beta galactosidase, beta lactamase, chloramphenicol acetyl transferase, or a fluorescent protein.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002082,assay,,,,Reporter_Gene_Assay,Class,Assay,Assay,RNA_Assay,,, electrochemiluminescence,"A method in which electromagnetic radiation, in the form of light emission, is generated from an electrochemical reaction in a solution.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C111193,assay,,,,Electrochemiluminescence,Class,Assay,Assay,RNA_Assay,,, -Real Time PCR,An application of PCR that measures the products generated during each cycle of the polymerase chain reaction process in order to determine the starting amount of template in the reaction.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C51962,assay,,,,Real_Time_PCR,Class,Assay,Assay,RNA_Assay,,, +real-time PCR,An application of PCR that measures the products generated during each cycle of the polymerase chain reaction process in order to determine the starting amount of template in the reaction.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C51962,assay,,,,Real_Time_PCR,Class,Assay,Assay,RNA_Assay,,, in vivo tumor growth,"The growth of a tumor measured using calipers, ruler, or another similar measurement device. See also """"in vivo bioluminescence"""".",,,FALSE,Sage Bionetworks,assay,,,,In_Vivo_Tumor_Growth,Class,Assay,Assay,Volume_Measurement_Assay,,, -Blood Chemistry Measurement,The determination of the measured concentrations of chemical constituents of the blood by assay in a clinical laboratory.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C47868,assay,,,,Blood_Chemistry_Measurement,Class,Assay,Assay,Clinical_Assay_Template,,, +blood chemistry measurement,The determination of the measured concentrations of chemical constituents of the blood by assay in a clinical laboratory.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C47868,assay,,,,Blood_Chemistry_Measurement,Class,Assay,Assay,Clinical_Assay_Template,,, in vivo bioluminescence,An imaging assay that allows detection of bioluminescence from a living organism or organisms.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0000651,assay,,,,In_Vivo_Bioluminescence,Class,Assay,Assay,Imaging_Assay,,, immunohistochemistry,An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001986,assay,,,,Immunohistochemistry,Class,Assay,Assay,Immuno_Assay,,, -NOMe-Seq,Nucleosome Occupancy and Methylome Sequencing,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C106053,assay,,,,NOMe-Seq,Class,Assay,Assay,Epigenetics_Assay,,, +NOMe-seq,Nucleosome Occupancy and Methylome Sequencing,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C106053,assay,,,,NOMe-Seq,Class,Assay,Assay,Epigenetics_Assay,,, FIA-MSMS,Flow injection analysis - tandem mass spectrometer,,,FALSE,https://www.ncbi.nlm.nih.gov/pubmed/28667829,assay,,,,FIA-MSMS,Class,Assay,Assay,Proteomics_Assay,,, -UPLC-MSMS,Ultra performance liquid chromatography - tandem mass spectrometer.,,,FALSE,https://www.wur.nl/en/show/Ultra-performance-liquid-chromatography-tandem-mass-spectrometer-UPLCMSMS.htm,assay,,,,UPLC-MSMS,Class,Assay,Assay,Proteomics_Assay,,, -HPLC-MSMS,"An analytical technique wherein high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C120691,assay,,,,HPLC-MSMS,Class,Assay,Assay,Proteomics_Assay,,, +ultra high-performance liquid chromatography/tandem mass spectrometry,"UPLC-MSMS is an analytical technique wherein ultra-high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C122176,assay,,,,Ultra_High-performance_Liquid_Chromatography_Tandem_Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, +high-performance liquid chromatography/tandem mass spectrometry,"HPLC-MSMS is an analytical technique wherein high performance liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C120691,assay,,,,High-performance_Liquid_Chromatography_Tandem_Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, liquid chromatography-electrochemical detection,"A liquid chromatography method that is sensitive to compounds which can be either reduced or oxidised. The mobile phase passes directly over the working electrode, which is set to the specific potential required for oxidation or reduction. The current produced is then measured.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0001746,assay,,,,Liquid_Chromatography-Electrochemical_Detection,Class,Assay,Assay,Proteomics_Assay,,, -rnaSeq,RNA Sequencing measurements,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001271,assay,,,,RNA-Seq,Class,Assay,Assay,RNA_Assay,,, -mirnaSeq,Small RNA measurements collected from RNA-Seq experiments,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002112,assay,,,,MiRNA-Seq,Class,Assay,Assay,RNA_Assay,,, -LC-MSMS,A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000701,assay,,,,LC-MSMS,Class,Assay,Assay,Proteomics_Assay,,, -LC-MS,A method where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterised by their mass-to-charge ratio and relative abundance,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000524,assay,,,,LC-MS,Class,Assay,Assay,Proteomics_Assay,,, -lncrnaSeq,Long non-coding RNA measurements collected from RNA-Seq experiments,,,FALSE,,assay,,,,LCRNA-Seq,Class,Assay,Assay,RNA_Assay,,, -Whole Exome Sequencing,A procedure that can determine the DNA sequence for all of the exons in an individual.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C101295,assay,,,,Whole_Exome_Sequencing,Class,Assay,Assay,DNA_Assay,,, +RNA-seq,RNA Sequencing measurements,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001271,assay,,,,RNA-Seq,Class,Assay,Assay,RNA_Assay,,, +miRNA-seq,Small RNA measurements collected from RNA sequencing experiments,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002112,assay,,,,MiRNA-Seq,Class,Assay,Assay,RNA_Assay,,, +liquid chromatography/tandem mass spectrometry,"LC-MSMS is an analytical technique wherein liquid chromatography is coupled to tandem mass spectrometry in order to separate, identify, and quantify substances in a sample.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C122168,assay,,,,Liquid_Chromatography_Tandem_Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, +liquid chromatography/mass spectrometry,"LC-MS is a hyphenated technique, combining the separation power of liquid chromatography (LC), an analytical chromatographic technique for separating ions or molecules dissolved in a solvent, with the detection power of mass spectrometry(MS), a technique to separate gas phase ions according their m/z (mass to charge ratio) value. Used for drug screening, pharmacology studies, environmental analyses and forensics.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C18475,assay,,,,Liquid_Chromatography_Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, +lncRNA-seq,Long non-coding RNA measurements collected from RNA-Seq experiments,,,FALSE,,assay,,,,LCRNA-Seq,Class,Assay,Assay,RNA_Assay,,, +whole exome sequencing,A procedure that can determine the DNA sequence for all of the exons in an individual.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C101295,assay,,,,Whole_Exome_Sequencing,Class,Assay,Assay,DNA_Assay,,, Sanger sequencing,"A DNA sequencing technique in which a mixture of deoxynucleosidetriphosphates (dNTPs) and chain-terminating dNTPs, which are radioactively or fluorescently labeled, are combined within the reaction mixture. Once the reaction is complete, the DNA strands are separated by size, and the labeled chain terminating dNTPs can be read in sequence by the investigator or by a machine.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C19641,assay,,,,Sanger_Sequencing,Class,Assay,Assay,DNA_Assay,,, -ChIPSeq,Chromatin immuno-precipitation followed by sequencing,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000716,assay,,,,ChIP-Seq,Class,Assay,Assay,Epigenetics_Assay,,, -rnaArray,RNA measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001463,assay,,,,RNA_Array,Class,Assay,Assay,RNA_Assay,,, -snpArray,SNP measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001204,assay,,,,SNP_Array,Class,Assay,Assay,DNA_Assay,,, -methylationArray,Methylation data captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001332,assay,,,,Methylation_Array,Class,Assay,Assay,Epigenetics_Assay,,, -mirnaArray,microRNA measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001335,assay,,,,MiRNA_Array,Class,Assay,Assay,RNA_Assay,,, -bisulfiteSeq,Methylation data captured by sequencing of DNA treated by a bisulfite-based chemical process,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000748,assay,,,,Bisulfite_Seq,Class,Assay,Assay,Epigenetics_Assay,,, -ATACSeq,Open chromatin regions measured by sequencing DNA after assay for transposase-accessible chromatin (ATAC) treatment,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002039,assay,,,,ATAC_Seq,Class,Assay,Assay,Epigenetics_Assay,,, +ChIP-seq,Chromatin immuno-precipitation followed by sequencing,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000716,assay,,,,ChIP-Seq,Class,Assay,Assay,Epigenetics_Assay,,, +RNA array,RNA measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001463,assay,,,,RNA_Array,Class,Assay,Assay,RNA_Assay,,, +SNP array,SNP measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001204,assay,,,,SNP_Array,Class,Assay,Assay,DNA_Assay,,, +methylation array,Methylation data captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001332,assay,,,,Methylation_Array,Class,Assay,Assay,Epigenetics_Assay,,, +miRNA array,microRNA measurements captured by array technology,,,FALSE,http://purl.obolibrary.org/obo/OBI_0001335,assay,,,,MiRNA_Array,Class,Assay,Assay,RNA_Assay,,, +bisulfite sequencing,Methylation data captured by sequencing of DNA treated by a bisulfite-based chemical process,,,FALSE,http://purl.obolibrary.org/obo/OBI_0000748,assay,,,,Bisulfite_Seq,Class,Assay,Assay,Epigenetics_Assay,,, +ATAC-seq,Open chromatin regions measured by sequencing DNA after assay for transposase-accessible chromatin (ATAC) treatment,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002039,assay,,,,ATAC_Seq,Class,Assay,Assay,Epigenetics_Assay,,, HI-C,Chromatin interactions detected by HI-C protocol,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0007693,assay,,,,HI-C,Class,Assay,Assay,Epigenetics_Assay,,, -errBisulfiteSeq,Data for enriched reduced representation bisulfite sequencing data,,,FALSE,,assay,,,,Err_Bisulfite_Seq,Class,Assay,Assay,Bisulfite_Seq,,, -ISOSeq,Full isoform sequencing,,,FALSE,,assay,,,,ISO-Seq,Class,Assay,Assay,RNA_Assay,,, -westernBlot,A multistep process in which a mixture of proteins is separated by gel electrophoresis,,,FALSE,http://purl.obolibrary.org/obo/MMO_0000338,assay,,,,Western_Blot,Class,Assay,Assay,Proteomics_Assay,,, -wholeGenomeSeq,Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time,,,FALSE,http://edamontology.org/topic_3673,assay,,,,Whole_Genome_Seq,Class,Assay,Assay,DNA_Assay,,, -polymeraseChainReaction,"A rapid technique for in vitro amplification of specific DNA or RNA sequences, allowing small quantities of short sequences to be analyzed without cloning",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000459,assay,,,,Polymerase_Chain_Reaction,Class,Assay,Assay,RNA_Assay,,, -cellViabilityAssay,This assay type measures the cellular state of living or dying by measuring an indicator of life or death,,,FALSE,http://www.bioassayontology.org/bao#BAO_0003009,assay,,,,Cell_Viability_Assay,Class,Assay,Assay,Cell_Assay,,, +ERR bisulfite sequencing,Enhanced reduced representation bisulfite sequencing (ERRBS) ,,,FALSE,,assay,,,,Err_Bisulfite_Seq,Class,Assay,Assay,Bisulfite_Seq,,, +ISO-seq,Full isoform sequencing,,,FALSE,,assay,,,,ISO-Seq,Class,Assay,Assay,RNA_Assay,,, +western blot,A multistep process in which a mixture of proteins is separated by gel electrophoresis,,,FALSE,http://purl.obolibrary.org/obo/MMO_0000338,assay,,,,Western_Blot,Class,Assay,Assay,Proteomics_Assay,,, +whole genome sequencing,Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time,,,FALSE,http://edamontology.org/topic_3673,assay,,,,Whole_Genome_Seq,Class,Assay,Assay,DNA_Assay,,, +polymerase chain reaction,"A rapid technique for in vitro amplification of specific DNA or RNA sequences, allowing small quantities of short sequences to be analyzed without cloning",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000459,assay,,,,Polymerase_Chain_Reaction,Class,Assay,Assay,RNA_Assay,,, +cell viability assay,This assay type measures the cellular state of living or dying by measuring an indicator of life or death,,,FALSE,http://www.bioassayontology.org/bao#BAO_0003009,assay,,,,Cell_Viability_Assay,Class,Assay,Assay,Cell_Assay,,, 2D Incucyte,Cell viability assay on a 2D monolayer model.,,,FALSE,,assay,,,,2D_Incucyte_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 2D CellTiter-Glo,Cell viability assay based on detection of ATP.,,,FALSE,https://www.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?catNum=G9241,assay,,,,2D_Cell_Titer_Glo_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 3D microtissue viability,Cell viability assay on a 3D microtissue model.,,,FALSE,https://www.ncbi.nlm.nih.gov/books/NBK343426/,assay,,,,3D_Microtissue_Viability_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, 2D AlamarBlue fluorescence,"Cell viability assay based on detection of AlamarBlue (resazurin). Living cells reduce blue, non-fluorescent resazurin to the red, fluorescent molecule resorufin. The amount of fluorescence or absorbance is proportional to the number of living cells and corresponds to the cell’s metabolic activity. For the fluorescence-based assay, color change and fluorescence can be detected using 560/590 nm (excitation/emission).",,,FALSE,https://www.thermofisher.com/us/en/home/life-science/cell-analysis/fluorescence-microplate-assays/microplate-assays-cell-viability/alamarblue-assay-cell-viability.html,assay,,,,2D_AlamarBlue_Fluorescence,Class,Assay,Assay,Cell_Viability_Assay,,, 2D AlamarBlue absorbance,"Cell viability assay based on detection of AlamarBlue (resazurin). Living cells reduce blue, non-fluorescent resazurin to the red, fluorescent molecule resorufin. The amount of fluorescence or absorbance is proportional to the number of living cells and corresponds to the cell’s metabolic activity. For the absorbance-based assay, absorbance can be read at 570 nm.",,,FALSE,https://www.thermofisher.com/us/en/home/life-science/cell-analysis/fluorescence-microplate-assays/microplate-assays-cell-viability/alamarblue-assay-cell-viability.html,assay,,,,2D_AlamarBlue_Absorbance,Class,Assay,Assay,Cell_Viability_Assay,,, in vivo PDX viability,Assay to assess viability using PDX model.,,,FALSE,,assay,,,,In_Vivo_PDX_Viability_Assay,Class,Assay,Assay,Cell_Viability_Assay,,, -atomicForceMicroscopy,Microscopy which uses a sharp spike (known as a 'tip') mounted on the end of a cantilever to scan the surface of the specimen,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000113,assay,,,,Atomic_Force_Microscopy,Class,Assay,Assay,Imaging_Assay,,, -brightfieldMicroscopy,Microscopy where the specimen is illuminated with light transmitted from a source on the opposite side of the specimen from the objective,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000104,assay,,,,Brightfield_Microscopy,Class,Assay,Assay,Imaging_Assay,,, -tractionForceMicroscopy,An experimental method for determining the tractions on the surface of a biological cell by obtaining measurements of the surrounding displacement field within an in vitro extracellular matrix (ECM),,,FALSE,https://en.wikipedia.org/wiki/Traction_force_microscopy,assay,,,,Traction_Force_Microscopy,Class,Assay,Assay,Imaging_Assay,,, -Phase-Contrast Microscopy,A simple non-quantitative form of interference microscopy of great utility in visualising live cells. Small differences in optical path length due to differences in refractive index and thickness of structures are visualised as differences in light intensity.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16857,assay,,,,Phase-Contrast_Microscopy,Class,Assay,Assay,Imaging_Assay,,, -nextGenerationTargetedSequencing,A type of next generation sequencing in which specific genes or portions of genes are targeted for sequencing using amplicon-based workflow.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C130177,assay,,,,NextGeneration_Targeted_Seq,Class,Assay,Assay,DNA_Assay,,, +atomic force microscopy,Microscopy which uses a sharp spike (known as a 'tip') mounted on the end of a cantilever to scan the surface of the specimen,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000113,assay,,,,Atomic_Force_Microscopy,Class,Assay,Assay,Imaging_Assay,,, +brightfield microscopy,Microscopy where the specimen is illuminated with light transmitted from a source on the opposite side of the specimen from the objective,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000104,assay,,,,Brightfield_Microscopy,Class,Assay,Assay,Imaging_Assay,,, +traction force microscopy,An experimental method for determining the tractions on the surface of a biological cell by obtaining measurements of the surrounding displacement field within an in vitro extracellular matrix (ECM),,,FALSE,https://en.wikipedia.org/wiki/Traction_force_microscopy,assay,,,,Traction_Force_Microscopy,Class,Assay,Assay,Imaging_Assay,,, +phase-contrast microscopy,A simple non-quantitative form of interference microscopy of great utility in visualising live cells. Small differences in optical path length due to differences in refractive index and thickness of structures are visualised as differences in light intensity.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16857,assay,,,,Phase-Contrast_Microscopy,Class,Assay,Assay,Imaging_Assay,,, +next generation targeted sequencing,A type of next generation sequencing in which specific genes or portions of genes are targeted for sequencing using amplicon-based workflow.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C130177,assay,,,,NextGeneration_Targeted_Seq,Class,Assay,Assay,DNA_Assay,,, MIB/MS,Kinomics assay using multiplexed kinase inhibitor beads and mass spectrometry (MIB/MS),,,FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328787/,assay,,,,MIB_MS,Class,Assay,Assay,Proteomics_Assay,,, -scCGIseq,"A method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs",,,FALSE,https://www.ncbi.nlm.nih.gov/pubmed/28126923,assay,,,,ScCGI_Seq,Class,Assay,Assay,Epigenetics_Assay,,, +scCGI-seq,"A method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs",,,FALSE,https://www.ncbi.nlm.nih.gov/pubmed/28126923,assay,,,,ScCGI_Seq,Class,Assay,Assay,Epigenetics_Assay,,, MudPIT,MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry,,,FALSE,http://purl.obolibrary.org/obo/MI_0658,assay,,,,MudPIT,Class,Assay,Assay,Proteomics_Assay,,, questionnaire,"A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0001000,assay,,,,Questionnaire,Class,Assay,Assay,Behavioral_Assay,,, DNA optical mapping,Fluorescent imaging of linearly extended DNA molecules to probe information patterns along the molecules,,,FALSE,https://doi.org/10.1016/j.copbio.2013.01.009,assay,,,,DNA_Optical_Mapping,Class,Assay,Assay,Imaging_Assay,,, -oxBS-Seq,Oxidative bisulfite sequencing (oxBS-Seq) to map 5-methylcytosine and 5-hydroxymethylcytosine,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008840,assay,,,,OxBS-Seq,Class,Assay,Assay,Epigenetics_Assay,,, -Ribo-Seq,Ribosome profiling (Ribo-Seq).,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008891,assay,,,,Ribo-Seq,Class,Assay,Assay,RNA-Seq,,, -Positron Emission Tomography,A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17007,assay,,,,Positron_Emission_Tomography,Class,Assay,Assay,Imaging_Assay,,, +oxBS-seq,Oxidative bisulfite sequencing (oxBS-Seq) to map 5-methylcytosine and 5-hydroxymethylcytosine,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008840,assay,,,,OxBS-Seq,Class,Assay,Assay,Epigenetics_Assay,,, +ribo-seq,Ribosome profiling (Ribo-Seq).,,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008891,assay,,,,Ribo-Seq,Class,Assay,Assay,RNA-Seq,,, +positron emission tomography,A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17007,assay,,,,Positron_Emission_Tomography,Class,Assay,Assay,Imaging_Assay,,, RPPA,Reverse phase protein array (RPPA) is a an assay that measures multiple protein expression levels in a large number of biological samples simultaneously using high quality antibodies,,,FALSE,http://www.bioassayontology.org/bao#BAO_0010030,assay,,,,RPPA,Class,Assay,Assay,Proteomics_Assay,,, ELISA,"A highly sensitive technique for detecting and measuring antigens or antibodies in a solution; the solution is run over a surface to which immobilized antibodies specific to the substance have been attached, and if the substance is present, it will bind to the antibody layer, and its presence is verified and visualized with an application of antibodies that have been tagged in some way.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16553,assay,,,,ELISA,Class,Assay,Assay,Proteomics_Assay,,, -LTP,Any measurable or observable characteristic related to the persistent robust synaptic response induced by synchronous stimulation of pre- and postsynaptic cells.,,,FALSE,http://purl.obolibrary.org/obo/VT_0002207,assay,,,,LTP,Class,Assay,Assay,Electrophysiology_Assay,,, -LFP,An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002189,assay,,,,LFP,Class,Assay,Assay,Electrophysiology_Assay,,, +long term potentiation assay,A measure of the persistent robust synaptic response induced by synchronous stimulation of pre- and postsynaptic cells.,,,FALSE,http://purl.obolibrary.org/obo/VT_0002207,assay,,,,Long_Term_Potentiation_Assay,Class,Assay,Assay,Electrophysiology_Assay,,, +local field potential recording,An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002189,assay,,,,Local_Field_Potential_Recording,Class,Assay,Assay,Electrophysiology_Assay,,, whole-cell patch clamp,"A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002178,assay,,,,Whole-cell_Patch_Clamp,Class,Assay,Assay,Cell_Assay,,, sandwich ELISA,"The sandwich ELISA measures the amount of antigen between two layers of antibodies. The antigens to be measured must contain at least two antigenic sites, capable of binding to antibody, since at least two antibodies act in the sandwich. So sandwich assays are restricted to the quantitation of multivalent antigens such as proteins or polysaccharides. Sandwich ELISAs for quantitation of antigens are especially valuable when the concentration of antigens is low and/or they are contained in high concentrations of contaminating protein.",,,FALSE,https://www.ebi.ac.uk/ols/ontologies/bao/terms?iri=http%3A%2F%2Fwww.bioassayontology.org%2Fbao%23BAO_0002421,assay,,,,Sandwich_ELISA,Class,Assay,Assay,ELISA,,, -Laser Speckle Imaging,"A noninvasive, non-scanning optical imaging technique that provides full-field visualization of blood flow to the tissue being imaged, which provides information about tissue perfusion and the efficiency of disease treatment.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C116492,assay,,,,Laser_Speckle_Imaging,Class,Assay,Assay,Imaging_Assay,,, -Genotyping,The determination of the DNA sequence of an individual.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C45447,assay,,,,Genotyping_Assay,Class,Assay,Assay,DNA_Assay,,, +laser speckle imaging,"A noninvasive, non-scanning optical imaging technique that provides full-field visualization of blood flow to the tissue being imaged, which provides information about tissue perfusion and the efficiency of disease treatment.",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C116492,assay,,,,Laser_Speckle_Imaging,Class,Assay,Assay,Imaging_Assay,,, +genotyping,The determination of the DNA sequence of an individual.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C45447,assay,,,,Genotyping_Assay,Class,Assay,Assay,DNA_Assay,,, TMT quantitation,"An isobaric labeling technique that uses tags containing four regions with the same total molecular weights and structure, so that during chromatographic or electrophoretic separation and in single MS mode, molecules labelled with different tags are indistinguishable.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0002175,assay,,,,TMT_Quantitation,Class,Assay,Assay,Proteomics_Assay,,, +mass spectrometry,"A generic mass spectrometry assay that allows identification and amount of peptide or protein materials.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0000708,assay,,,,Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, label free mass spectrometry,"A mass spectrometry assay that allows for measurement for endogenous targets in live cell assays, and eliminates the need for tags, dyes, or specialized reagents or engineered cells.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0000708,assay,,,,Label_Free_Mass_Spectrometry,Class,Assay,Assay,Proteomics_Assay,,, cell count,A procedure to determine the number of cells in a sample. Also used to mean the result of such a procedure.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C48938,assay,,,,Cell_Count,Class,Assay,Assay,Cell_Assay,,, -immunoAssay,Generic immunology assay,,immunoAssayType,FALSE,,assay,,,,Immuno_Assay,Class,Assay,Assay,Assay,,, -Conventional MRI,"Magnetic resonance imaging using standard protocols for high resolution structural and anatomic characterization, including T1 weighted, T2 weighted, fluid attenuated inversion recovery (FLAIR), and gadolinium-enhanced sequences. [ NCI ]",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C175525,assay,,,,Conventional_MRI,Class,Assay,Assay,MRI_Assay,,, -Functional MRI,The principle of functional MRI imaging is to take a series of images of an organ in quick succession and to statistically analyze the images for differences among them. Most commonly used in studies of brain function. [ NCI ],,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17958,assay,,,,Functional_MRI,Class,Assay,Assay,MRI_Assay,,, -Magnetic Resonance Spectroscopy,Detection and measurement of the resonant spectra of molecular species in a tissue or sample.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16810,assay,,,,Magnetic_Resonance_Spectroscopy,Class,Assay,Assay,Radio_Assay,,, -FTIR Spectroscopy,"Fourier transform infrared (FTIR) spectroscopy is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid or gas. An FTIR spectrometer simultaneously collects high-resolution spectral data over a wide spectral range.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000636,assay,,,,FTIR_Spectroscopy,Class,Assay,Assay,Proteomics_Assay,,, +immunoassay,Generic immunology assay,,immunoAssayType,FALSE,,assay,,,,Immuno_Assay,Class,Assay,Assay,Assay,,, +conventional MRI,"Magnetic resonance imaging using standard protocols for high resolution structural and anatomic characterization, including T1 weighted, T2 weighted, fluid attenuated inversion recovery (FLAIR), and gadolinium-enhanced sequences. [ NCI ]",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C175525,assay,,,,Conventional_MRI,Class,Assay,Assay,MRI_Assay,,, +functional MRI,The principle of functional MRI imaging is to take a series of images of an organ in quick succession and to statistically analyze the images for differences among them. Most commonly used in studies of brain function. [ NCI ],,,FALSE,http://purl.obolibrary.org/obo/NCIT_C17958,assay,,,,Functional_MRI,Class,Assay,Assay,MRI_Assay,,, +magnetic resonance spectroscopy,Detection and measurement of the resonant spectra of molecular species in a tissue or sample.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C16810,assay,,,,Magnetic_Resonance_Spectroscopy,Class,Assay,Assay,Radio_Assay,,, +FTIR spectroscopy,"Fourier transform infrared (FTIR) spectroscopy is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid or gas. An FTIR spectrometer simultaneously collects high-resolution spectral data over a wide spectral range.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000636,assay,,,,FTIR_Spectroscopy,Class,Assay,Assay,Proteomics_Assay,,, rheometry,The study of the flow of fluids which cannot be defined by a single value of viscosity. Rheometry (synonym: rheology) is the measurement of the relationship between deformation and stress for these liquids. [ https://orcid.org/0000-0002-0640-0422 ],,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000915,assay,,,,Rheometry,Class,Assay,Assay,Assay,,, -Gel filtration chromatography,"Gel filtration chromatography (synonym: gel permeation chromatography - GPC) is a type of size-exclusion chromatography (SEC), that separates analytes on the basis of size, typically in organic solvents. The technique is often used for the analysis of polymers.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0001011,assay,,,,Gel_Filtration_Chromatography,Class,Assay,Assay,Proteomics_Assay,,, +gel filtration chromatography,"Gel filtration chromatography (synonym: gel permeation chromatography - GPC) is a type of size-exclusion chromatography (SEC), that separates analytes on the basis of size, typically in organic solvents. The technique is often used for the analysis of polymers.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0001011,assay,,,,Gel_Filtration_Chromatography,Class,Assay,Assay,Proteomics_Assay,,, differential scanning calorimetry,"Differential scanning calorimetry (DSC) is the measurement of thermodynamic parameters (e.g. enthalpy) during a chemical or biochemical reaction of both a sample and a reference, by the known variation (step-wise or linear) of one variable, whilst a second is kept constant.",,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000684,assay,,,,Differential_Scanning_Calorimetry,Class,Assay,Assay,Assay,,, -singleMolecule,An experiment in which a single molecule was used in an assay,,,FALSE,,drugScreenType,,,,Single_Molecule_Drug_Screen,Class,Assay,Assay,Drug_Screen,,, -smallMoleculeLibraryScreen,"High throughput sample analysis of small molecules for purpose such as drug discovery, or biochemical, genetic or pharmacological tests.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0001726,drugScreenType,,,,Small_Molecule_Library_Screen,Class,Assay,Assay,Drug_Screen,,, -combinationLibraryScreen,High throughput sample analysis of collections of compounds that provide a variety of chemically diverse structures that can be used to identify structure types that have affinity with pharmacological targets.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0001686,drugScreenType,,,,Combination_Library_Screen,Class,Assay,Assay,Drug_Screen,,, -combinationScreen,,,,FALSE,,drugScreenType,,,,Combination_Screen,Class,Assay,Assay,Drug_Screen,,, -compoundScreen,,,,FALSE,,assay,,,,Compound_Screen,Class,Assay,Assay,Drug_Screen,,, +single molecule drug screen assay,An experiment in which a single molecule was used in an assay,,,FALSE,,drugScreenType,,,,Single_Molecule_Drug_Screen,Class,Assay,Assay,Drug_Screen,,, +small molecule library screen,"High throughput sample analysis of small molecules for purpose such as drug discovery, or biochemical, genetic or pharmacological tests.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0001726,drugScreenType,,,,Small_Molecule_Library_Screen,Class,Assay,Assay,Drug_Screen,,, +combination library screen,High throughput sample analysis of collections of compounds that provide a variety of chemically diverse structures that can be used to identify structure types that have affinity with pharmacological targets.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0001686,drugScreenType,,,,Combination_Library_Screen,Class,Assay,Assay,Drug_Screen,,, +combination screen,,,,FALSE,,drugScreenType,,,,Combination_Screen,Class,Assay,Assay,Drug_Screen,,, +compound screen,,,,FALSE,,assay,,,,Compound_Screen,Class,Assay,Assay,Drug_Screen,,, array,,,,FALSE,,assay,,,,Array,Class,Assay,Assay,Assay,,, -Single Cell RNA Sequencing,A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C171152,assay,,,,ScRNA_Seq,Class,Assay,Assay,RNA-Seq,,, +single-cell RNA-seq,A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C171152,assay,,,,ScRNA_Seq,Class,Assay,Assay,RNA-Seq,,, spatial transcriptomics,"assay that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections",,,FALSE,http://www.ebi.ac.uk/efo/EFO_0008994,assay,,,,Spatial_Transcriptomics,Class,Assay,Assay,RNA-Seq,,, -Massively Parallel Reporter Assay,An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002675,assay,,,,Massively_Parallel_Reporter_Assay,Class,Assay,Assay,Reporter_Gene_Assay,,, +massively parallel reporter assay,An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002675,assay,,,,Massively_Parallel_Reporter_Assay,Class,Assay,Assay,Reporter_Gene_Assay,,, Riccardi and Ablon scales,"The Riccardi and Ablon scales score severity and visibility of disease, respectively, and are commonly used as a combined assessment for NF1 patients in clinical settings. See https://doi.org/10.1001/archderm.137.11.1421 for example usage.",,,FALSE,https://doi.org/10.1001/archderm.137.11.1421,assay,,,,Riccardi_Ablon_Scales,Class,Assay,Assay,Clinical_Assay,,, -Spatial Frequency Domain Imaging,"Spatial Frequency Domain Imaging (SFDI) is a non-contact, depth-varying and wide-field optical imaging technique for measuring optical properties in a wide field-of-view on a pixel-by-pixel basis. Relevant applications include including burn assessment, skin tissue evaluation, tumor tissue detection, brain tissue monitoring.",,,FALSE,https://doi.org/10.3390/photonics8050162,assay,,,,Spatial_Frequency_Domain_Imaging,Class,Assay,Assay,Imaging_Assay,,,Note that term has no matches in OLS as of June 2022. -Optical Coherence Tomography,"Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C20828,assay,,,,Optical_Coherence_Tomography,Class,Assay,Assay,Imaging_Assay,,, +spatial frequency domain imaging,"Spatial Frequency Domain Imaging (SFDI) is a non-contact, depth-varying and wide-field optical imaging technique for measuring optical properties in a wide field-of-view on a pixel-by-pixel basis. Relevant applications include including burn assessment, skin tissue evaluation, tumor tissue detection, brain tissue monitoring.",,,FALSE,https://doi.org/10.3390/photonics8050162,assay,,,,Spatial_Frequency_Domain_Imaging,Class,Assay,Assay,Imaging_Assay,,,Note that term has no matches in OLS as of June 2022. +optical coherence tomography,"Optical Coherence Tomography (OCT) combines the principles of ultrasound with the imaging performance of a microscope. OCT uses infrared light waves that reflect off the internal microstructure within the biological tissues. The frequencies and bandwidths of infrared light are orders of magnitude higher than medical ultrasound signals, resulting in greatly increased image resolution, 8-25 times greater than any existing modality. In addition to providing high-level resolutions for the evaluation of microanatomic structures OCT is also able to provide information regarding tissue composition",,,FALSE,http://purl.obolibrary.org/obo/NCIT_C20828,assay,,,,Optical_Coherence_Tomography,Class,Assay,Assay,Imaging_Assay,,, CUT&RUN,"Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. (doi:10.7554/eLife.21856)",,,FALSE,,assay,,,,CUT_RUN,Class,Assay,Assay,Epigenetics_Assay,,, -3D Imaging,"Technique to produce 3D images to visualize important structures in great detail. To produce 3D images, many scans are made, and then combined by computers to produce a 3D model, which can then be manipulated. 3D ultrasounds are produced using a somewhat similar technique.",,Assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C18485,assay,,,,3D_Imaging,Class,Assay,Assay,Imaging_Assay,,, -High Frequency Ultrasound,"High frequency ultrasound (HFUS) is an imaging modality that can give greater resolution of surface changes in skin (review in PMID:24583666)",,Assay,FALSE,,assay,,,,High_Frequency_Ultrasound,Class,Assay,Assay,Imaging_Assay,,, -Dynamic Light Scattering,"Dynamic Light Scattering (DLS), also known as photocorrelation spectroscopy, is a method for determining the size distribution of a sample of small particles in solution by illuminating the sample with a light source (usually a laser) and measuring the time-dependent fluctuations in the intensity of the scattered light caused by Brownian motion.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000167,assay,,,,Dynamic_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,, -Static Light Scattering,"Static Light Scattering is a method for determining structure by measuring the total or time-averaged scattering intensity of scattered visible light as a function of angle.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000180,assay,,,,Static_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,, -Light Scattering Assay,"A method for determining structure by measuring the change in direction or energy of scattered visible light. Light is scattered by the electrons surrounding the atomic nuclei in the sample.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000166,assay,,,,Light_Scattering_Assay,Class,Assay,Assay,Spectroscopy,,, +3D imaging,"Technique to produce 3D images to visualize important structures in great detail. To produce 3D images, many scans are made, and then combined by computers to produce a 3D model, which can then be manipulated. 3D ultrasounds are produced using a somewhat similar technique.",,Assay,FALSE,http://purl.obolibrary.org/obo/NCIT_C18485,assay,,,,3D_Imaging,Class,Assay,Assay,Imaging_Assay,,, +high frequency ultrasound,"High frequency ultrasound (HFUS) is an imaging modality that can give greater resolution of surface changes in skin (review in PMID:24583666)",,Assay,FALSE,,assay,,,,High_Frequency_Ultrasound,Class,Assay,Assay,Imaging_Assay,,, +dynamic light scattering,"Dynamic Light Scattering (DLS), also known as photocorrelation spectroscopy, is a method for determining the size distribution of a sample of small particles in solution by illuminating the sample with a light source (usually a laser) and measuring the time-dependent fluctuations in the intensity of the scattered light caused by Brownian motion.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000167,assay,,,,Dynamic_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,, +static light scattering,"Static Light Scattering is a method for determining structure by measuring the total or time-averaged scattering intensity of scattered visible light as a function of angle.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000180,assay,,,,Static_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,, +light scattering assay,"A method for determining structure by measuring the change in direction or energy of scattered visible light. Light is scattered by the electrons surrounding the atomic nuclei in the sample.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000166,assay,,,,Light_Scattering_Assay,Class,Assay,Assay,Spectroscopy,,, flow cytometry,"A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution",,,FALSE,http://purl.obolibrary.org/obo/OBI_0000916,assay,,,,Flow_Cytometry_Assay,Class,Assay,Assay,Assay,,, -Pattern electroretinogram,"Pattern electroretinogram (PERG) is an electrophysiologic ophthalmologic test that provides non-invasive objective, quantitative measurement of central retinal function. PERG is the retinal response to a pattern-reversing, black-and-white checkerboard or stripped stimulus. The PERG assesses both macular and retinal ganglion cell electrical activity and can help differentiate between diseases of macular versus optic nerve dysfunction.",,,FALSE,https://www.ncbi.nlm.nih.gov/books/NBK560641,assay,,,,Pattern_Electroretinogram,Class,Assay,Assay,Assay,,, -Optokinetic reflex assay,"The optokinetic reflex (OKR), which serves to stabilize a moving image on the retina, is a behavioral response that has many favorable attributes as a test of CNS function. The OKR requires no training, assesses the function of diverse CNS circuits, can be induced repeatedly with minimal fatigue or adaptation, and produces an electronic record that is readily and objectively quantifiable.",,,FALSE,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002055,assay,,,,SUSHI,Class,Assay,Assay,Assay,,, +pattern electroretinogram,"Pattern electroretinogram (PERG) is an electrophysiologic ophthalmologic test that provides non-invasive objective, quantitative measurement of central retinal function. PERG is the retinal response to a pattern-reversing, black-and-white checkerboard or stripped stimulus. The PERG assesses both macular and retinal ganglion cell electrical activity and can help differentiate between diseases of macular versus optic nerve dysfunction.",,,FALSE,https://www.ncbi.nlm.nih.gov/books/NBK560641,assay,,,,Pattern_Electroretinogram,Class,Assay,Assay,Assay,,, +optokinetic reflex assay,"The optokinetic reflex (OKR), which serves to stabilize a moving image on the retina, is a behavioral response that has many favorable attributes as a test of CNS function. The OKR requires no training, assesses the function of diverse CNS circuits, can be induced repeatedly with minimal fatigue or adaptation, and produces an electronic record that is readily and objectively quantifiable.",,,FALSE,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002055,assay,,,,SUSHI,Class,Assay,Assay,Assay,,, SUSHI,"Fast super-resolution method that exploits sparsity in the underlying vasculature and statistical independence within the measured signals to detect slow-flowing blood, facilitating noninvasive perfusion measurements.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/30295619/,assay,,,,Optokinetic_Reflex_Assay,Class,Assay,Assay,Assay,,, 3D confocal imaging,"Confocal microscopy with 3D reconstruction of the sample tissue.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/34331281,assay,,,,3D_Confocal_Imaging,Class,Assay,Assay,Imaging_Assay,,, 3D electron microscopy,"Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,3D_Electron_Microscopy,Class,Assay,Assay,Imaging_Assay,,, @@ -107,4 +108,15 @@ cell competition,"An assay in which two or more labeled populations of cells or body size trait measurement,"Any measurable or observable characteristic related to the overall physical magnitude of an organism.",,,FALSE,http://purl.obolibrary.org/obo/VT_0100005,assay,,,,Body_Size_Trait_Measurement,Class,Assay,Assay,Imaging_Assay,,, twin spot assay,"Two individual and genetically different populations of cells that originate from the same mitotic recombination event; twin spots allow a direct and reliable comparison between mutant and wild-type clones, and the size of the wild-type twin can serve as a reference for comparison with the homozygous mutant clones.",,,FALSE,https://pubmed.ncbi.nlm.nih.gov/29378809/,assay,,,,Twin_Spot_Assay,Class,Assay,Assay,Imaging_Assay,,, perineurial cell thickness,"Measuring the thickness of the cells in the perineurium, e.g. in developing Drosophila melanogaster.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,Perineurial_Cell_Thickness,Class,Assay,Assay,Imaging_Assay,,, -survival,"Any quantitative measurement of survival of or in an individual or study population.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,Perineurial_Cell_Thickness,Class,Assay,Assay,Imaging_Assay,,, +survival,"Any quantitative measurement of survival of or in an individual or study population.",,,FALSE,http://purl.obolibrary.org/obo/MI_0410,assay,,,,Perineurial_Cell_Thickness,Class,Assay,Assay,Assay,,, +gait measurement,"Quantification of some aspect of a person's gait such as rhythm, variability or step length",,,FALSE,http://www.ebi.ac.uk/efo/EFO_0007680,assay,,,,Gait_Measurement,Class,Assay,Assay,Physiology_Assay,,, +sorbitol dehydrogenase activity level assay,"An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0003434,assay,,,,Sorbitol_Dehydrogenase_Activity_Level_Assay,Class,Assay,Assay,Cell_Assay,,, +T cell receptor repertoire sequencing,"A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample.",,,FALSE,http://purl.obolibrary.org/obo/OBI_0002990,assay,,,,T_Cell_Receptor_Repertoire_Sequencing,Class,Assay,Assay,DNA_Assay,,, +cell proliferation,"A cellular assay that allows for the measurement of the multiplication or reproduction of cells, resulting in the expansion of a cell population.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0000636,assay,,,,Cell_Proliferation,Class,Assay,Assay,Cell_Assay,,, +oxygen consumption assay,"Assay measuring oxygen consumption rate (OCR) to assess changes in metabolism in e.g. cancer cells",,,FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275291/,assay,,,,Oxygen_Consumption_Assay,Class,Assay,Assay,Cell_Assay,,, +reactive oxygen species assay,"Reactive oxygen species (ROS) are measured to assess oxidative events and to investigate their biological importance using antioxidants or inhibitors to modulate the phenomena observed.",,,FALSE,https://www.nature.com/articles/s42255-022-00591-z,assay,,,,Reactive_Oxygen_Species_Assay,Class,Assay,Assay,Cell_Assay,,,See also https://www.nature.com/articles/s42255-022-00591-z for good discussion +ATPase activity assay,"As an assay used for drug discovery, measures enzymatic ATP hydrolysis to help assess levels of enzymatic activity induced by a candidate drug molecule.",,,FALSE,http://purl.obolibrary.org/obo/MI_0880,assay,,,,ATPase_Activity_Assay,Class,Assay,Assay,Cell_Assay,,,See also https://www.bellbrooklabs.com/atpase-activity-assay-for-drug-discovery/ for discussion +novelty response behavior assay,"A behavioral assay devised to measure novelty response behavior",,,FALSE,,assay,,,,Novelty_Response_Behavior_Assay,Class,Assay,Assay,Behavioral_Assay,,, +contextual conditioning behavior assay,"A behavioral assay devised to measure contextual conditioning behavior",,,FALSE,,assay,,,,Contextual_Conditioning_Behavior_Assay,Class,Assay,Assay,Behavioral_Assay,,, +active avoidance learning behavior assay,"A behavioral assay devised to measure active avoidance learning behavior",,,FALSE,,assay,,,,Active_Avoidance_Learning Behavior_Assay,Class,Assay,Assay,Behavioral_Assay,,, +focus forming assay,"The focus forming assay (FFA) is an immunostaining technique and a variation of the viral plaque assay. Instead of detecting the plaque formation after virus-induced cell lysis these assays detect infected host cells and infectious virus particles before a plaque is formed.",,,FALSE,,assay,,,,Focus_Forming_Assay,Class,Assay,Assay,Viral_Assay,,,See https://www.bpes.co.uk/focus-forming-assay-virus-titer-quantitation/ diff --git a/modules/Assay/annotationProperty.csv b/modules/Assay/annotationProperty.csv index 91993bb6..336a9c06 100644 --- a/modules/Assay/annotationProperty.csv +++ b/modules/Assay/annotationProperty.csv @@ -1,6 +1,6 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,,,drugScreenType,Property,Assay,annotationProperty,,,, -assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography,CUT&RUN,High Frequency Ultrasound, 3D Imaging,Dynamic Light Scattering,Static Light Scattering,flow cytometry,Pattern electroretinogram,Optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy,cell competition,body size trait measurement,twin spot assay,perineurial cell thickness,survival,Phase-Contrast Microscopy",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, +assay,The technology used to generate the data in this file,"HPLC,elevated plus maze test,open field test,rotarod performance test,mRNA counts,high content screen,immunocytochemistry,immunofluorescence,autoradiography,reporter gene assay,electrochemiluminescence,real-time PCR,in vivo tumor growth,blood chemistry measurement,in vivo bioluminescence,immunohistochemistry,NOMe-seq,FIA-MSMS,ultra high-performance liquid chromatography/tandem mass spectrometry,high-performance liquid chromatography/tandem mass spectrometry,liquid chromatography-electrochemical detection,RNA-seq,miRNA-seq,liquid chromatography/tandem mass spectrometry,liquid chromatography/mass spectrometry,lncRNA-seq,whole exome sequencing,Sanger sequencing,ChIP-seq,RNA array,SNP array,methylation array,miRNA array,bisulfite sequencing,ATAC-seq,HI-C,ERR bisulfite sequencing,ISO-seq,western blot,whole genome sequencing,polymerase chain reaction,cell viability assay,2D Incucyte,2D CellTiter-Glo,3D microtissue viability,2D AlamarBlue fluorescence,2D AlamarBlue absorbance,in vivo PDX viability,atomic force microscopy,brightfield microscopy,traction force microscopy,phase-contrast microscopy,next generation targeted sequencing,MIB/MS,scCGI-seq,MudPIT,questionnaire,DNA optical mapping,oxBS-seq,ribo-seq,positron emission tomography,RPPA,ELISA,long term potentiation assay,local field potential recording,whole-cell patch clamp,sandwich ELISA,laser speckle imaging,genotyping,TMT quantitation,mass spectrometry,label free mass spectrometry,cell count,immunoassay,conventional MRI,functional MRI,magnetic resonance spectroscopy,FTIR spectroscopy,rheometry,gel filtration chromatography,differential scanning calorimetry,single molecule drug screen assay,small molecule library screen,combination library screen,combination screen,compound screen,array,single-cell RNA-seq,spatial transcriptomics,massively parallel reporter assay,Riccardi and Ablon scales,spatial frequency domain imaging,optical coherence tomography,CUT&RUN,3D imaging,high frequency ultrasound,dynamic light scattering,static light scattering,light scattering assay,flow cytometry,pattern electroretinogram,optokinetic reflex assay,SUSHI,3D confocal imaging,3D electron microscopy,cell competition,body size trait measurement,twin spot assay,perineurial cell thickness,survival,gait measurement,sorbitol dehydrogenase activity level assay,T cell receptor repertoire sequencing,cell proliferation,oxygen consumption assay,reactive oxygen species assay,ATPase activity assay,novelty response behavior assay,contextual conditioning behavior assay,active avoidance learning behavior assay,focus forming assay",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","Illumina HiSeq 3000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina NextSeq 500, Illumina HiSeq 2000, Illumina MiSeq, Zeiss LSM 980, Affymetrix Genome-Wide Human SNP 5.0 Array, Affymetrix Genome-Wide Human SNP 6.0 Array, PacBio RS II, Illumina Genome Analyzer IIx, Illumina HumanOmni1-Quadv1.0, Illumina 1M, Illumina h650, Illumina Omni2pt5M, Illumina Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen 300Karray, Agilent 44Karray, Illumina WholeGenome DASL, Illumina HumanHap300, Nanostring Counter, LTQ Orbitrap XL, Illumina HumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, Affymetrix U133AB, Affymetrix Human Gene 1.0 ST Array, Affymetrix Human Genome U133 Plus 2.0 Array, Illumina HiSeq X, Bionano Irys, Infinium HumanOmniExpressExome, Illumina NextSeq 550, Illumina NextSeq 1000, Illumina NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, Nanostring GeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression,Cherry Imaging TRACE Platform,Cherry Imaging FACE Platform,LifeViz Micro System,LifeViz Infinity System,BGISEQ-500",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, targetCaptureKitID,"A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.",,,TRUE,http://purl.obolibrary.org/obo/NCIT_C177583,experimentalData,,,,targetCaptureKitID,Property,Assay,annotationProperty,,,,"For WES processing, the target BED used could be provided based on the target capture kit." libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,, @@ -8,7 +8,7 @@ assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,F proteinExtractSource,Source of the extracted protein used in the experiment,"cell lysate, nuclei, mitochondria, cytoplasm",,TRUE,http://purl.obolibrary.org/obo/OBI_0000894,experimentalData,,,,proteinExtractSource,Property,Assay,annotationProperty,,,, reporterGene,"A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.",,,FALSE,,experimentalData,,,,reporterGene,Property,Assay,annotationProperty,,,, reporterSubstance,A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.,,,FALSE,,experimentalData,,,,reporterSubstance,Property,Assay,annotationProperty,,,, -immunoAssayType,Type of immuno assay,"ChIPseq, ATAC-seq",,TRUE,,immunoAssay,,,,immunoAssayType,Property,Assay,annotationProperty,,,, +immunoAssayType,Type of immuno assay,"ChIP-seq, ATAC-seq",,TRUE,,immunoAssay,,,,immunoAssayType,Property,Assay,annotationProperty,,,, runType,Is the sequencing run single or paired end?,"singleEnd, pairedEnd","readPair,isStranded,readPairOrientation,readStrandOrigin,readLength,readDepth",FALSE,Sage Bionetworks,ngs,,,,runType,Property,Assay,annotationProperty,ngsParameter,Run_Type,, readPair,The read of origin,,,FALSE,,ngs,,,int,readPair,Property,Assay,annotationProperty,ngsParameter,Read_Pair,, isStranded,Whether or not the library is stranded (Yes; No),"Yes, No",,FALSE,,ngs,,,,isStranded,Property,Assay,annotationProperty,ngsParameter,,, diff --git a/registered-json-schemas/superdataset.json b/registered-json-schemas/superdataset.json index 560e04d4..9f2d1e42 100644 --- a/registered-json-schemas/superdataset.json +++ b/registered-json-schemas/superdataset.json @@ -10,110 +10,122 @@ "2D Incucyte", "3D confocal imaging", "3D electron microscopy", - "3D Imaging", + "3D imaging", "3D microtissue viability", + "active avoidance learning behavior assay", "array", - "ATACSeq", - "atomicForceMicroscopy", + "ATAC-seq", + "atomic force microscopy", + "ATPase activity assay", "autoradiography", - "bisulfiteSeq", - "Blood Chemistry Measurement", + "bisulfite sequencing", + "blood chemistry measurement", "body size trait measurement", - "brightfieldMicroscopy", + "brightfield microscopy", "cell competition", "cell count", - "cellViabilityAssay", - "ChIPSeq", - "combinationLibraryScreen", - "combinationScreen", - "compoundScreen", - "Conventional MRI", + "cell proliferation", + "cell viability assay", + "ChIP-seq", + "combination library screen", + "combination screen", + "compound screen", + "contextual conditioning behavior assay", + "conventional MRI", "CUT&RUN", "differential scanning calorimetry", "DNA optical mapping", - "Dynamic Light Scattering", + "dynamic light scattering", "electrochemiluminescence", "elevated plus maze test", "ELISA", - "errBisulfiteSeq", + "ERR bisulfite sequencing", "FIA-MSMS", "flow cytometry", - "FTIR Spectroscopy", - "Functional MRI", - "Gel filtration chromatography", - "Genotyping", + "focus forming assay", + "FTIR spectroscopy", + "functional MRI", + "gait measurement", + "gel filtration chromatography", + "genotyping", "HI-C", "high content screen", - "High Frequency Ultrasound", + "high frequency ultrasound", + "high-performance liquid chromatography/tandem mass spectrometry", "HPLC", - "HPLC-MSMS", - "immunoAssay", - "Immunocytochemistry", + "immunoassay", + "immunocytochemistry", "immunofluorescence", "immunohistochemistry", "in vivo bioluminescence", "in vivo PDX viability", "in vivo tumor growth", - "ISOSeq", + "ISO-seq", "label free mass spectrometry", - "Laser Speckle Imaging", - "LC-MS", - "LC-MSMS", - "LFP", - "Light Scattering Assay", + "laser speckle imaging", + "light scattering assay", "liquid chromatography-electrochemical detection", - "lncrnaSeq", - "LTP", - "Magnetic Resonance Spectroscopy", - "Massively Parallel Reporter Assay", - "methylationArray", + "liquid chromatography/mass spectrometry", + "liquid chromatography/tandem mass spectrometry", + "lncRNA-seq", + "local field potential recording", + "long term potentiation assay", + "magnetic resonance spectroscopy", + "massively parallel reporter assay", + "mass spectrometry", + "methylation array", "MIB/MS", - "mirnaArray", - "mirnaSeq", - "mRNAcounts", + "miRNA array", + "miRNA-seq", + "mRNA counts", "MudPIT", - "nextGenerationTargetedSequencing", - "NOMe-Seq", + "next generation targeted sequencing", + "NOMe-seq", + "novelty response behavior assay", "open field test", - "Optical Coherence Tomography", - "Optokinetic reflex assay", - "oxBS-Seq", - "Pattern electroretinogram", + "optical coherence tomography", + "optokinetic reflex assay", + "oxBS-seq", + "oxygen consumption assay", + "pattern electroretinogram", "perineurial cell thickness", - "Phase-Contrast Microscopy", - "polymeraseChainReaction", - "Positron Emission Tomography", + "phase-contrast microscopy", + "polymerase chain reaction", + "positron emission tomography", "questionnaire", - "Real Time PCR", + "reactive oxygen species assay", + "real-time PCR", "reporter gene assay", "rheometry", - "Ribo-Seq", + "ribo-seq", "Riccardi and Ablon scales", - "rnaArray", - "rnaSeq", + "RNA array", + "RNA-seq", "rotarod performance test", "RPPA", "sandwich ELISA", "Sanger sequencing", - "scCGIseq", - "Single Cell RNA Sequencing", - "singleMolecule", - "smallMoleculeLibraryScreen", - "snpArray", - "Spatial Frequency Domain Imaging", + "scCGI-seq", + "single-cell RNA-seq", + "single molecule drug screen assay", + "small molecule library screen", + "SNP array", + "sorbitol dehydrogenase activity level assay", + "spatial frequency domain imaging", "spatial transcriptomics", - "Static Light Scattering", + "static light scattering", "survival", "SUSHI", + "T cell receptor repertoire sequencing", "TMT quantitation", - "tractionForceMicroscopy", + "traction force microscopy", "twin spot assay", - "UPLC-MSMS", - "westernBlot", + "ultra high-performance liquid chromatography/tandem mass spectrometry", + "western blot", "whole-cell patch clamp", - "Whole Exome Sequencing", - "wholeGenomeSeq" - ] + "whole exome sequencing", + "whole genome sequencing" + ] } }, "if": {