From 585bceb8eb8d2c451a8075691c6e39fdb8b09066 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Tue, 9 Jul 2024 12:03:00 -0500 Subject: [PATCH 1/4] Add three CRISPR assays --- src/ontology/modules/assays.owl | 143 ++++++++++++++++++++++++++++++ src/ontology/templates/assays.tsv | 3 + 2 files changed, 146 insertions(+) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index d7454e09..a9ec11ca 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -21909,6 +21909,12 @@ + + + + + + @@ -26567,6 +26573,143 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR screening assay + An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. + Bjoern Peters + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR screening assay + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR screen using single RNA-Seq + An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression + Bjoern Peters + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR screen using single RNA-Seq + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR perturbation screen using FISH and flow cytometry + An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes + Bjoern Peters + Jennifer Jou + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR perturbation screen using FISH and flow cytometry + + + + diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 8679701b..56a4b328 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -656,6 +656,9 @@ OBI:0003599 single cell T cell receptor repertoire sequencing assay single cell OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay QCM An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. http://www.ncbi.nlm.nih.gov/pubmed/23504432|https://en.wikipedia.org/wiki/Quartz_crystal_microbalance Randi Vita|Bjoern Peters|Sebastian Duesing subclass assay OBI:0003604 multiplexed error-robust fluorescence in situ hybridization assay MERFISH A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1724 subclass fluorescence in-situ hybridization assay OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. https://doi.org/10.21769/BioProtoc.3070 Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1725 subclass fluorescence in-situ hybridization assay +OBI:0003659 in vitro CRISPR screening assay in vitro CRISPR screening assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell +OBI:0003660 in vitro CRISPR screen using single RNA-Seq in vitro CRISPR screen using single RNA-Seq An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay single-cell RNA sequencing assay +OBI:0003661 in vitro CRISPR perturbation screen using FISH and flow cytometry in vitro CRISPR perturbation screen using FISH and flow cytometry An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay flow cytometry assay|fluorescence in-situ hybridization assay OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course From a29d3b58b385a02a22a26f6d5904933ae6cc43cd Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Thu, 18 Jul 2024 10:43:23 -0500 Subject: [PATCH 2/4] Edit label of OBI:0003660 --- src/ontology/modules/assays.owl | 4 ++-- src/ontology/templates/assays.tsv | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index a9ec11ca..736011ac 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -26658,13 +26658,13 @@ - in vitro CRISPR screen using single RNA-Seq + in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 Jennifer Jou - in vitro CRISPR screen using single RNA-Seq + in vitro CRISPR screen using single-cell RNA-seq diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 56a4b328..dd09d688 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -657,7 +657,7 @@ OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay OBI:0003604 multiplexed error-robust fluorescence in situ hybridization assay MERFISH A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1724 subclass fluorescence in-situ hybridization assay OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. https://doi.org/10.21769/BioProtoc.3070 Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1725 subclass fluorescence in-situ hybridization assay OBI:0003659 in vitro CRISPR screening assay in vitro CRISPR screening assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell -OBI:0003660 in vitro CRISPR screen using single RNA-Seq in vitro CRISPR screen using single RNA-Seq An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay single-cell RNA sequencing assay +OBI:0003660 in vitro CRISPR screen using single-cell RNA-seq in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay single-cell RNA sequencing assay OBI:0003661 in vitro CRISPR perturbation screen using FISH and flow cytometry in vitro CRISPR perturbation screen using FISH and flow cytometry An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay flow cytometry assay|fluorescence in-situ hybridization assay OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') From 6be7836c4575a5cbbdfdc404e1781b7f2d45e1a1 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Fri, 16 Aug 2024 11:45:18 -0500 Subject: [PATCH 3/4] Add fourth assay term and standardize labels --- src/ontology/modules/assays.owl | 132 +++++++++++++++++++----------- src/ontology/templates/assays.tsv | 7 +- 2 files changed, 89 insertions(+), 50 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 736011ac..8a3beeff 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -26630,13 +26630,13 @@ - in vitro CRISPR screening assay + in vitro CRISPR screen assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 Jennifer Jou - in vitro CRISPR screening assay + in vitro CRISPR screen assay @@ -26644,22 +26644,26 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + in vitro CRISPR screen using single-cell RNA-seq - An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression + An in vitro CRISPR screen assay that uses single-cell RNA-Seq to detect induced changes in gene expression. Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 @@ -26672,40 +26676,74 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - in vitro CRISPR perturbation screen using FISH and flow cytometry - An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes + + + + + + + + + + + + + + + + + + + in vitro CRISPR perturbation screen using flow cytometry + An in vitro CRISPR screen assay that uses flow cytometry to detect induced changes in gene expression of the targeted genes. Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 Jennifer Jou - in vitro CRISPR perturbation screen using FISH and flow cytometry + in vitro CRISPR screen using flow cytometry + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry + An in vitro CRISPR screen assay that uses fluorescence imaging-based reporter gene detection and flow cytometry to detect induced changes in gene expression of the targeted genes. + Jennifer Jou + Sebastian Duesing + https://github.com/obi-ontology/obi/issues/1784 + Jennifer Jou + in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index dd09d688..3676eb62 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -656,9 +656,10 @@ OBI:0003599 single cell T cell receptor repertoire sequencing assay single cell OBI:0003601 quartz crystal microbalance assay quartz crystal microbalance assay QCM An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator. http://www.ncbi.nlm.nih.gov/pubmed/23504432|https://en.wikipedia.org/wiki/Quartz_crystal_microbalance Randi Vita|Bjoern Peters|Sebastian Duesing subclass assay OBI:0003604 multiplexed error-robust fluorescence in situ hybridization assay MERFISH A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging. https://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization#MERFISH Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1724 subclass fluorescence in-situ hybridization assay OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution. https://doi.org/10.21769/BioProtoc.3070 Sebastian Duesing Brain Image Library https://github.com/obi-ontology/obi/issues/1725 subclass fluorescence in-situ hybridization assay -OBI:0003659 in vitro CRISPR screening assay in vitro CRISPR screening assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell -OBI:0003660 in vitro CRISPR screen using single-cell RNA-seq in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screening assay that uses single cell RNA-Seq to detect induced changes in gene expression Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay single-cell RNA sequencing assay -OBI:0003661 in vitro CRISPR perturbation screen using FISH and flow cytometry in vitro CRISPR perturbation screen using FISH and flow cytometry An in vitro CRISPR screening assay that uses single FISH and flow cytometry to detect induced changes in gene expression of the targeted genes Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass in vitro CRISPR screening assay flow cytometry assay|fluorescence in-situ hybridization assay +OBI:0003659 in vitro CRISPR screen assay in vitro CRISPR screen assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell +OBI:0003660 in vitro CRISPR screen using single-cell RNA-seq in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screen assay that uses single-cell RNA-Seq to detect induced changes in gene expression. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay single-cell RNA sequencing assay +OBI:0003661 in vitro CRISPR screen using flow cytometry in vitro CRISPR perturbation screen using flow cytometry An in vitro CRISPR screen assay that uses flow cytometry to detect induced changes in gene expression of the targeted genes. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay flow cytometry assay +OBI:0003668 in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry An in vitro CRISPR screen assay that uses fluorescence imaging-based reporter gene detection and flow cytometry to detect induced changes in gene expression of the targeted genes. Jennifer Jou|Sebastian Duesing Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay flow cytometry assay|fluorescence imaging-based reporter gene assay OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course From a0a07c077919129e0aa654017685a511c95f5819 Mon Sep 17 00:00:00 2001 From: Sebastian Duesing <66700705+sebastianduesing@users.noreply.github.com> Date: Mon, 19 Aug 2024 14:32:19 -0500 Subject: [PATCH 4/4] Remove OBI:0003668 --- src/ontology/modules/assays.owl | 43 ------------------------------- src/ontology/templates/assays.tsv | 1 - 2 files changed, 44 deletions(-) diff --git a/src/ontology/modules/assays.owl b/src/ontology/modules/assays.owl index 8a3beeff..88cee146 100644 --- a/src/ontology/modules/assays.owl +++ b/src/ontology/modules/assays.owl @@ -26705,49 +26705,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry - An in vitro CRISPR screen assay that uses fluorescence imaging-based reporter gene detection and flow cytometry to detect induced changes in gene expression of the targeted genes. - Jennifer Jou - Sebastian Duesing - https://github.com/obi-ontology/obi/issues/1784 - Jennifer Jou - in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry - - - - diff --git a/src/ontology/templates/assays.tsv b/src/ontology/templates/assays.tsv index 3676eb62..8ea6c7ed 100644 --- a/src/ontology/templates/assays.tsv +++ b/src/ontology/templates/assays.tsv @@ -659,7 +659,6 @@ OBI:0003605 single molecule fluorescence in situ hybridization smFISH A fluore OBI:0003659 in vitro CRISPR screen assay in vitro CRISPR screen assay An assay in which cells expressing a Cas system are infected with a library of guide RNAs with the intent of causing a perturbation at the target of the guide RNAs. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 subclass assay cas mediated mutagenesis assay cell OBI:0003660 in vitro CRISPR screen using single-cell RNA-seq in vitro CRISPR screen using single-cell RNA-seq An in vitro CRISPR screen assay that uses single-cell RNA-Seq to detect induced changes in gene expression. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay single-cell RNA sequencing assay OBI:0003661 in vitro CRISPR screen using flow cytometry in vitro CRISPR perturbation screen using flow cytometry An in vitro CRISPR screen assay that uses flow cytometry to detect induced changes in gene expression of the targeted genes. Jennifer Jou|Bjoern Peters Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay flow cytometry assay -OBI:0003668 in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry in vitro CRISPR screen using fluorescence imaging-based reporter gene and flow cytometry An in vitro CRISPR screen assay that uses fluorescence imaging-based reporter gene detection and flow cytometry to detect induced changes in gene expression of the targeted genes. Jennifer Jou|Sebastian Duesing Jennifer Jou https://github.com/obi-ontology/obi/issues/1784 equivalent in vitro CRISPR screen assay flow cytometry assay|fluorescence imaging-based reporter gene assay OBI:0302736 comet assay ready for release single cell gel electrophoresis assay|SCGE assay An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis PMID:7686265 PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay. Philippe Rocca-Serra subclass assay fluorescence microscopy assay cell ('material entity' and ('has role' some 'dye role') and ('bearer of' some fluorescence)) agarose gel information content entity cellular response to DNA damage stimulus OBI:0302737 PCR-SSCP assay ready for release polymerase chain reaction-single strand conformation polymorphism assay An assay that identifies DNA sequence variation (mutation, deletion, insertions) in target DNA sequences amplified using polymerase chain reaction using gel electrophoresis and denaturating conditions PMID:18219595 PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Philippe Rocca-Serra subclass genotyping assay polymerase chain reaction|material component separation amplified DNA (image and 'genotype information') OBI:0600002 tumor grading pending final vetting grading of tumor An assay that determines the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus. OBI branch derived; submitted by MO Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney subclass assay specimen disease course