add oncotree terms (#103)

allaway · anngvu · web-flow · commit cc62c57c9ed0 · 2022-02-03T13:39:59.000-07:00
* add oncotree terms

* Regen docs only for new tumors from ONCOTREE

Co-authored-by: Anh Nguyet Vu &lt;anngvu@gmail.com&gt;
diff --git a/NF.csv b/NF.csv
diff --git a/NF.jsonld b/NF.jsonld
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/templates/Clinical_Assay_Template.csv b/docs/templates/Clinical_Assay_Template.csv
@@ -18,7 +18,7 @@
 "tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
 "cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
 "tumorType","The type of tumor that the biospecimen used to generate the data were collected from. ","optional","#Tumor",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin). ","optional","",""
+"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
 "experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
 "InChIKey","A unique hash key for a compound, e.g. for “Selumetinib”, the key is CYOHGALHFOKKQC-UHFFFAOYSA-N (https://pubchem.ncbi.nlm.nih.gov/compound/10127622#section=InChI-Key). This is a more reliable identifier than the compound name and should be used if available.","optional","",""
diff --git a/docs/templates/Epigenetics_Assay_Template.csv b/docs/templates/Epigenetics_Assay_Template.csv
@@ -24,7 +24,7 @@
 "cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
 "tumorType","The type of tumor that the biospecimen used to generate the data were collected from. ","optional","#Tumor",""
 "assayTarget","The HUGO gene symbol that represents the target analyte assayed.","optional","",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin). ","optional","",""
+"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
 "experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
 "platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
diff --git a/docs/templates/Genomics_Assay_Template.csv b/docs/templates/Genomics_Assay_Template.csv
@@ -24,7 +24,7 @@
 "cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
 "tumorType","The type of tumor that the biospecimen used to generate the data were collected from. ","optional","#Tumor",""
 "specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin). ","optional","",""
+"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
 "experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
 "platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
diff --git a/docs/templates/Imaging_Assay_Template.csv b/docs/templates/Imaging_Assay_Template.csv
@@ -24,7 +24,7 @@
 "cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
 "tumorType","The type of tumor that the biospecimen used to generate the data were collected from. ","optional","#Tumor",""
 "assayTarget","The HUGO gene symbol that represents the target analyte assayed.","optional","",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin). ","optional","",""
+"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
 "experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
 "platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
diff --git a/docs/templates/MRI_Assay_Template.csv b/docs/templates/MRI_Assay_Template.csv
@@ -16,7 +16,7 @@
 "tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue",""
 "nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
 "nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin). ","optional","",""
+"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
 "experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
 "platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
diff --git a/docs/templates/Patient_Timepoints_Template.csv b/docs/templates/Patient_Timepoints_Template.csv
@@ -5,7 +5,7 @@
 "diagnosis","A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.","optional","#Diagnosis","Currently a single NF diagnosis allowed; in the future multiple diagnoses may be allowed for comorbidities."
 "nf1Genotype","Genotype of NF1 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
 "nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin). ","optional","",""
+"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
 "experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
 "comments","Brief free-text comments that may also be important to understanding the data. ","optional","",""
diff --git a/docs/templates/Pharmacokinetics_Assay_Template.csv b/docs/templates/Pharmacokinetics_Assay_Template.csv
@@ -24,7 +24,7 @@
 "cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
 "tumorType","The type of tumor that the biospecimen used to generate the data were collected from. ","optional","#Tumor",""
 "assayTarget","The HUGO gene symbol that represents the target analyte assayed.","optional","",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin). ","optional","",""
+"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
 "experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
 "experimentId","When applicable, an optional identifier that can be used to distinguish or group the experiments that generated the data; also can be used to denote internal batch reference if needed.","optional","",""
diff --git a/docs/templates/Plate_Based_Reporter_Assay_Template.csv b/docs/templates/Plate_Based_Reporter_Assay_Template.csv
@@ -26,7 +26,7 @@
 "platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
 "reporterGene","A biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences.","optional","",""
 "reporterSubstance","A gene which produces an easily assayed phenotype. Often used for expression studies of heterologous promoters.","optional","",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin). ","optional","",""
+"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
 "experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
 "comments","Brief free-text comments that may also be important to understanding the data. ","optional","",""
diff --git a/docs/templates/Proteomics_Assay_Template.csv b/docs/templates/Proteomics_Assay_Template.csv
@@ -24,7 +24,7 @@
 "isPrimaryCell","Boolean flag indicating whether or not cellType is primary  (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE",""
 "cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell",""
 "tumorType","The type of tumor that the biospecimen used to generate the data were collected from. ","optional","#Tumor",""
-"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin). ","optional","",""
+"experimentalCondition","A free-text description of the experimental condition (e.g. 5 mM doxorubicin).","optional","",""
 "experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""
 "platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
