diff --git a/.github/workflows/test-on-PR.yaml b/.github/workflows/test-on-PR.yaml
index e9549a97..75950b88 100644
--- a/.github/workflows/test-on-PR.yaml
+++ b/.github/workflows/test-on-PR.yaml
@@ -6,6 +6,9 @@ on:
name: test-coverage
+env:
+ DISPLAY: 0.0
+
jobs:
test-coverage:
runs-on: ubuntu-latest
diff --git a/DESCRIPTION b/DESCRIPTION
index 29a9a6ac..29c22b0a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -9,6 +9,7 @@ Authors@R: c(
person("Madison","Feshuk",role = "ctb",email = "feshuk.madison@epa.gov", comment = c(ORCID = "0000-0002-1390-6405")),
person("Lori","Kolaczkowski",role = "ctb",email = "kolaczkowski.lori@epa.gov"),
person("Kurt", "Dunham", role = "ctb", email = "dunham.kurt@epa.gov"),
+ person("Carter", "Thunes", role = "ctb", email = "thunes.carter@epa.gov"),
person("Todd", "Zurlinden", role="ctb"),
person("Parth", "Kothiya", role = "ctb"),
person("Woodrow R", "Setzer", role = "ctb"),
diff --git a/LICENSE b/LICENSE
index db4f2edc..1f1d9fd8 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2022
+YEAR: 2023
COPYRIGHT HOLDER: U.S. Federal Government
diff --git a/LICENSE.md b/LICENSE.md
index 7abd29c5..884e4b26 100644
--- a/LICENSE.md
+++ b/LICENSE.md
@@ -1,6 +1,6 @@
# MIT License
-Copyright (c) 2022 U.S. Federal Government
+Copyright (c) 2023 U.S. Federal Government
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
diff --git a/R/tcplDefine.R b/R/tcplDefine.R
index 3505ef0c..5a9ff127 100644
--- a/R/tcplDefine.R
+++ b/R/tcplDefine.R
@@ -50,59 +50,36 @@
#' @export
tcplDefine <- function(val = NULL) {
+
+ tbl = c("invitrodb_dd")
- drvr <- getOption("TCPL_DRVR")
+ qformat <- "SELECT invitrodb_table, invitrodb_field, description FROM invitrodb_dd"
- # example driver
- if (drvr == "example"){
+ if (!is.null(val)) {
- dd <- invitrodb_dd[]
+ vstring <- paste0("\"", val, "\"", collapse = ",")
+ qformat <- paste(qformat, "WHERE invitrodb_table IN (%s) OR invitrodb_field IN (%s);")
+ qstring <- sprintf(qformat, vstring, vstring)
- if (!is.null(val)) {
- dd <- dd[dd$invitrodb_table %in% val | dd$invitrodb_field %in% val,]
-
- if (nrow(dd) == 0) {
- warning("The given table and/or field names were not found.")
- }
- }
+ } else {
- return(dd)
+ qstring <- paste0(qformat, ";")
}
- # MySQL driver
- if (drvr != "example") {
-
- tbl = c("invitrodb_dd")
-
- qformat <- "SELECT invitrodb_table, invitrodb_field, description FROM invitrodb_dd"
-
- if (!is.null(val)) {
-
- vstring <- paste0("\"", val, "\"", collapse = ",")
- qformat <- paste(qformat, "WHERE invitrodb_table IN (%s) OR invitrodb_field IN (%s);")
- qstring <- sprintf(qformat, vstring, vstring)
-
- } else {
-
- qstring <- paste0(qformat, ";")
-
- }
-
- dat <- tcplQuery(query = qstring, db = getOption("TCPL_DB"), tbl=tbl)
+
+ dat <- tcplQuery(query = qstring, db = getOption("TCPL_DB"), tbl=tbl)
+
+ if (!is.null(val)) {
- if (!is.null(val)) {
-
- if (nrow(dat) == 0) {
- warning("The given table and/or field names were not found.")
- return(dat[])
- }
-
+ if (nrow(dat) == 0) {
+ warning("The given table and/or field names were not found.")
+ return(dat[])
}
- dat[]
-
}
+ dat[]
+
}
#-------------------------------------------------------------------------------
diff --git a/R/tcplQuery.R b/R/tcplQuery.R
index 22464aa1..585081a6 100644
--- a/R/tcplQuery.R
+++ b/R/tcplQuery.R
@@ -55,7 +55,13 @@ tcplQuery <- function(query, db = getOption("TCPL_DB"),
}
result <- as.data.table(sqldf(query, stringsAsFactors=F))
-
+
+ }
+
+ if (drvr == "example") {
+ db_pars <- "Using example data"
+
+ result <- as.data.table(sqldf(query, stringsAsFactors=F))
}
diff --git a/tests/testthat/_snaps/tcplDefine.md b/tests/testthat/_snaps/tcplDefine.md
index b966a0d8..2818e3a2 100644
--- a/tests/testthat/_snaps/tcplDefine.md
+++ b/tests/testthat/_snaps/tcplDefine.md
@@ -1,206 +1,175 @@
# empty returns full dictionary
- Code
- tcplDefine()
- Output
- invitrodb_table invitrodb_field
- 1: sc0 s0id
- 2: sc0 acid
- 3: sc0 spid
- 4: sc0 apid
- 5: sc0 rowi
- 6: sc0 coli
- 7: sc0 wllt
- 8: sc0 wllq
- 9: sc0 conc
- 10: sc0 rval
- 11: sc0 srcf
- 12: sc1 s1id
- 13: sc1 s0id
- 14: sc1 acid
- 15: sc1 aeid
- 16: sc1 logc
- 17: sc1 bval
- 18: sc1 pval
- 19: sc1 resp
- 20: mc0 m0id
- 21: mc0 acid
- 22: mc0 spid
- 23: mc0 apid
- 24: mc0 rowi
- 25: mc0 coli
- 26: mc0 wllt
- 27: mc0 wllq
- 28: mc0 conc
- 29: mc0 rval
- 30: mc0 srcf
- 31: mc1 m1id
- 32: mc1 m0id
- 33: mc1 acid
- 34: mc1 cndx
- 35: mc1 repi
- 36: chemical chid
- 37: chemical casn
- 38: chemical chnm
- 39: chemical dsstox_substance_id
- 40: sample spid
- 41: sample chid
- 42: sample stkc
- 43: sample stkc_unit
- 44: sample tested_conc_unit
- invitrodb_table invitrodb_field
- description
- 1: Level 0 ID
- 2: Assay component ID
- 3: Sample ID
- 4: Assay plate ID
- 5: Assay plate row index
- 6: Assay plate column index
- 7: Well type, where: t, Test compound; c, Gain-of-signal control in multiple concentrations; p, Gain-of-signal control in single concentration; n, Neutral/negative control; m, Loss-of-signal control in multiple concentrations; o, Loss-of-signal control in single concentration; b, Blank well; and v, Viability control.
- 8: 1 if the well quality was good, else 0
- 9: Concentration is micromolar
- 10: Raw assay component value/readout from vendor
- 11: Filename of the source file containing the data
- 12: Level 1 ID
- 13: Level 0 ID
- 14: Assay component ID
- 15: Assay component endpoint ID
- 16: Log base 10 concentration
- 17: Baseline value
- 18: Positive control value
- 19: Normalized response value
- 20: Level 0 ID
- 21: Assay component ID
- 22: Sample ID
- 23: Assay plate ID
- 24: Assay plate row index
- 25: Assay plate column index
- 26: Well type, where: t, Test compound; c, Gain-of-signal control in multiple concentrations; p, Gain-of-signal control in single concentration; n, Neutral/negative control; m, Loss-of-signal control in multiple concentrations; o, Loss-of-signal control in single concentration; b, Blank well; and v, Viability control.
- 27: 1 if the well quality was good, else 0
- 28: Concentration is micromolar
- 29: Raw assay component value/readout from vendor
- 30: Filename of the source file containing the data
- 31: Level 1 ID
- 32: Level 0 ID
- 33: Assay component ID
- 34: Concentration index
- 35: Replicate index
- 36: Chemical ID
- 37: CAS Registry Number
- 38: Chemical name
- 39: Unique identifier from U.S. EPA Distributed Structure-Searchable Toxicity (DSSTox) Database
- 40: Sample ID
- 41: Chemical ID
- 42: Stock concentration
- 43: Stock concentration unit
- 44: The concentration unit for the concentration values in the data-containing tables
- description
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# multiple values returns all necessary definitions
- Code
- tcplDefine(c("chemical", "sample"))
- Output
- invitrodb_table invitrodb_field
- 1: chemical chid
- 2: chemical casn
- 3: chemical chnm
- 4: chemical dsstox_substance_id
- 5: sample spid
- 6: sample chid
- 7: sample stkc
- 8: sample stkc_unit
- 9: sample tested_conc_unit
- description
- 1: Chemical ID
- 2: CAS Registry Number
- 3: Chemical name
- 4: Unique identifier from U.S. EPA Distributed Structure-Searchable Toxicity (DSSTox) Database
- 5: Sample ID
- 6: Chemical ID
- 7: Stock concentration
- 8: Stock concentration unit
- 9: The concentration unit for the concentration values in the data-containing tables
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---
- Code
- tcplDefine(c("spid", "rval", "wllt"))
- Output
- invitrodb_table invitrodb_field
- 1: sc0 spid
- 2: sc0 wllt
- 3: sc0 rval
- 4: mc0 spid
- 5: mc0 wllt
- 6: mc0 rval
- 7: sample spid
- description
- 1: Sample ID
- 2: Well type, where: t, Test compound; c, Gain-of-signal control in multiple concentrations; p, Gain-of-signal control in single concentration; n, Neutral/negative control; m, Loss-of-signal control in multiple concentrations; o, Loss-of-signal control in single concentration; b, Blank well; and v, Viability control.
- 3: Raw assay component value/readout from vendor
- 4: Sample ID
- 5: Well type, where: t, Test compound; c, Gain-of-signal control in multiple concentrations; p, Gain-of-signal control in single concentration; n, Neutral/negative control; m, Loss-of-signal control in multiple concentrations; o, Loss-of-signal control in single concentration; b, Blank well; and v, Viability control.
- 6: Raw assay component value/readout from vendor
- 7: Sample ID
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+ bmNlbnRyYXRpb247IG4sIE5ldXRyYWwvbmVnYXRpdmUgY29udHJvbDsgbSwgTG9zcy1vZi1z
+ aWduYWwgY29udHJvbCBpbiBtdWx0aXBsZSBjb25jZW50cmF0aW9uczsgbywgTG9zcy1vZi1z
+ aWduYWwgY29udHJvbCBpbiBzaW5nbGUgY29uY2VudHJhdGlvbjsgYiwgQmxhbmsgd2VsbDsg
+ YW5kIHYsIFZpYWJpbGl0eSBjb250cm9sLgAEAAkAAAAtUmF3IGFzc2F5IGNvbXBvbmVudCB2
+ YWx1ZS9yZWFkb3V0IGZyb20gdmVuZG9yAAQACQAAAAlTYW1wbGUgSUQAAAQCAAAAAQAEAAkA
+ AAAJcm93Lm5hbWVzAAAADQAAAAKAAAAA////+QAABAIAAAABAAQACQAAAAVjbGFzcwAAABAA
+ AAACAAQACQAAAApkYXRhLnRhYmxlAAQACQAAAApkYXRhLmZyYW1lAAAEAgAAAAEABAAJAAAA
+ ES5pbnRlcm5hbC5zZWxmcmVmAAAAFgAAABYAAAD+AAAA/gAAABAAAAADAAQACQAAAA9pbnZp
+ dHJvZGJfdGFibGUABAAJAAAAD2ludml0cm9kYl9maWVsZAAEAAkAAAALZGVzY3JpcHRpb24A
+ AAQCAAAAAQAEAAkAAAAFbmFtZXMAAAAQAAAAAwAEAAkAAAAPaW52aXRyb2RiX3RhYmxlAAQA
+ CQAAAA9pbnZpdHJvZGJfZmllbGQABAAJAAAAC2Rlc2NyaXB0aW9uAAAA/g==
---
- Code
- tcplDefine(c("sc0", "chid"))
- Output
- invitrodb_table invitrodb_field
- 1: sc0 s0id
- 2: sc0 acid
- 3: sc0 spid
- 4: sc0 apid
- 5: sc0 rowi
- 6: sc0 coli
- 7: sc0 wllt
- 8: sc0 wllq
- 9: sc0 conc
- 10: sc0 rval
- 11: sc0 srcf
- 12: chemical chid
- 13: sample chid
- description
- 1: Level 0 ID
- 2: Assay component ID
- 3: Sample ID
- 4: Assay plate ID
- 5: Assay plate row index
- 6: Assay plate column index
- 7: Well type, where: t, Test compound; c, Gain-of-signal control in multiple concentrations; p, Gain-of-signal control in single concentration; n, Neutral/negative control; m, Loss-of-signal control in multiple concentrations; o, Loss-of-signal control in single concentration; b, Blank well; and v, Viability control.
- 8: 1 if the well quality was good, else 0
- 9: Concentration is micromolar
- 10: Raw assay component value/readout from vendor
- 11: Filename of the source file containing the data
- 12: Chemical ID
- 13: Chemical ID
+ WAoAAAACAAQCAgACAwAAAAMTAAAAAwAAABAAAAANAAQACQAAAANzYzAABAAJAAAAA3NjMAAE
+ AAkAAAADc2MwAAQACQAAAANzYzAABAAJAAAAA3NjMAAEAAkAAAADc2MwAAQACQAAAANzYzAA
+ BAAJAAAAA3NjMAAEAAkAAAADc2MwAAQACQAAAANzYzAABAAJAAAAA3NjMAAEAAkAAAAIY2hl
+ bWljYWwABAAJAAAABnNhbXBsZQAAABAAAAANAAQACQAAAARzMGlkAAQACQAAAARhY2lkAAQA
+ CQAAAARzcGlkAAQACQAAAARhcGlkAAQACQAAAARyb3dpAAQACQAAAARjb2xpAAQACQAAAAR3
+ bGx0AAQACQAAAAR3bGxxAAQACQAAAARjb25jAAQACQAAAARydmFsAAQACQAAAARzcmNmAAQA
+ CQAAAARjaGlkAAQACQAAAARjaGlkAAAAEAAAAA0ABAAJAAAACkxldmVsIDAgSUQABAAJAAAA
+ EkFzc2F5IGNvbXBvbmVudCBJRAAEAAkAAAAJU2FtcGxlIElEAAQACQAAAA5Bc3NheSBwbGF0
+ ZSBJRAAEAAkAAAAVQXNzYXkgcGxhdGUgcm93IGluZGV4AAQACQAAABhBc3NheSBwbGF0ZSBj
+ b2x1bW4gaW5kZXgABAAJAAABO1dlbGwgdHlwZSwgd2hlcmU6IHQsIFRlc3QgY29tcG91bmQ7
+ IGMsIEdhaW4tb2Ytc2lnbmFsIGNvbnRyb2wgaW4gbXVsdGlwbGUgY29uY2VudHJhdGlvbnM7
+ IHAsIEdhaW4tb2Ytc2lnbmFsIGNvbnRyb2wgaW4gc2luZ2xlIGNvbmNlbnRyYXRpb247IG4s
+ IE5ldXRyYWwvbmVnYXRpdmUgY29udHJvbDsgbSwgTG9zcy1vZi1zaWduYWwgY29udHJvbCBp
+ biBtdWx0aXBsZSBjb25jZW50cmF0aW9uczsgbywgTG9zcy1vZi1zaWduYWwgY29udHJvbCBp
+ biBzaW5nbGUgY29uY2VudHJhdGlvbjsgYiwgQmxhbmsgd2VsbDsgYW5kIHYsIFZpYWJpbGl0
+ eSBjb250cm9sLgAEAAkAAAAmMSBpZiB0aGUgd2VsbCBxdWFsaXR5IHdhcyBnb29kLCBlbHNl
+ IDAABAAJAAAAG0NvbmNlbnRyYXRpb24gaXMgbWljcm9tb2xhcgAEAAkAAAAtUmF3IGFzc2F5
+ IGNvbXBvbmVudCB2YWx1ZS9yZWFkb3V0IGZyb20gdmVuZG9yAAQACQAAAC9GaWxlbmFtZSBv
+ ZiB0aGUgc291cmNlIGZpbGUgY29udGFpbmluZyB0aGUgZGF0YQAEAAkAAAALQ2hlbWljYWwg
+ SUQABAAJAAAAC0NoZW1pY2FsIElEAAAEAgAAAAEABAAJAAAACXJvdy5uYW1lcwAAAA0AAAAC
+ gAAAAP////MAAAQCAAAAAQAEAAkAAAAFY2xhc3MAAAAQAAAAAgAEAAkAAAAKZGF0YS50YWJs
+ ZQAEAAkAAAAKZGF0YS5mcmFtZQAABAIAAAABAAQACQAAABEuaW50ZXJuYWwuc2VsZnJlZgAA
+ ABYAAAAWAAAA/gAAAP4AAAAQAAAAAwAEAAkAAAAPaW52aXRyb2RiX3RhYmxlAAQACQAAAA9p
+ bnZpdHJvZGJfZmllbGQABAAJAAAAC2Rlc2NyaXB0aW9uAAAEAgAAAAEABAAJAAAABW5hbWVz
+ AAAAEAAAAAMABAAJAAAAD2ludml0cm9kYl90YWJsZQAEAAkAAAAPaW52aXRyb2RiX2ZpZWxk
+ AAQACQAAAAtkZXNjcmlwdGlvbgAAAP4=
# one value returns all necessary definitions
- Code
- tcplDefine("chemical")
- Output
- invitrodb_table invitrodb_field
- 1: chemical chid
- 2: chemical casn
- 3: chemical chnm
- 4: chemical dsstox_substance_id
- description
- 1: Chemical ID
- 2: CAS Registry Number
- 3: Chemical name
- 4: Unique identifier from U.S. EPA Distributed Structure-Searchable Toxicity (DSSTox) Database
+ WAoAAAACAAQCAgACAwAAAAMTAAAAAwAAABAAAAAEAAQACQAAAAhjaGVtaWNhbAAEAAkAAAAI
+ Y2hlbWljYWwABAAJAAAACGNoZW1pY2FsAAQACQAAAAhjaGVtaWNhbAAAABAAAAAEAAQACQAA
+ AARjaGlkAAQACQAAAARjYXNuAAQACQAAAARjaG5tAAQACQAAABNkc3N0b3hfc3Vic3RhbmNl
+ X2lkAAAAEAAAAAQABAAJAAAAC0NoZW1pY2FsIElEAAQACQAAABNDQVMgUmVnaXN0cnkgTnVt
+ YmVyAAQACQAAAA1DaGVtaWNhbCBuYW1lAAQACQAAAFtVbmlxdWUgaWRlbnRpZmllciBmcm9t
+ IFUuUy4gRVBBIERpc3RyaWJ1dGVkIFN0cnVjdHVyZS1TZWFyY2hhYmxlIFRveGljaXR5IChE
+ U1NUb3gpIERhdGFiYXNlAAAEAgAAAAEABAAJAAAACXJvdy5uYW1lcwAAAA0AAAACgAAAAP//
+ //wAAAQCAAAAAQAEAAkAAAAFY2xhc3MAAAAQAAAAAgAEAAkAAAAKZGF0YS50YWJsZQAEAAkA
+ AAAKZGF0YS5mcmFtZQAABAIAAAABAAQACQAAABEuaW50ZXJuYWwuc2VsZnJlZgAAABYAAAAW
+ AAAA/gAAAP4AAAAQAAAAAwAEAAkAAAAPaW52aXRyb2RiX3RhYmxlAAQACQAAAA9pbnZpdHJv
+ ZGJfZmllbGQABAAJAAAAC2Rlc2NyaXB0aW9uAAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAA
+ AAMABAAJAAAAD2ludml0cm9kYl90YWJsZQAEAAkAAAAPaW52aXRyb2RiX2ZpZWxkAAQACQAA
+ AAtkZXNjcmlwdGlvbgAAAP4=
---
- Code
- tcplDefine("spid")
- Output
- invitrodb_table invitrodb_field description
- 1: sc0 spid Sample ID
- 2: mc0 spid Sample ID
- 3: sample spid Sample ID
+ WAoAAAACAAQCAgACAwAAAAMTAAAAAwAAABAAAAADAAQACQAAAANzYzAABAAJAAAAA21jMAAE
+ AAkAAAAGc2FtcGxlAAAAEAAAAAMABAAJAAAABHNwaWQABAAJAAAABHNwaWQABAAJAAAABHNw
+ aWQAAAAQAAAAAwAEAAkAAAAJU2FtcGxlIElEAAQACQAAAAlTYW1wbGUgSUQABAAJAAAACVNh
+ bXBsZSBJRAAABAIAAAABAAQACQAAAAlyb3cubmFtZXMAAAANAAAAAoAAAAD////9AAAEAgAA
+ AAEABAAJAAAABWNsYXNzAAAAEAAAAAIABAAJAAAACmRhdGEudGFibGUABAAJAAAACmRhdGEu
+ ZnJhbWUAAAQCAAAAAQAEAAkAAAARLmludGVybmFsLnNlbGZyZWYAAAAWAAAAFgAAAP4AAAD+
+ AAAAEAAAAAMABAAJAAAAD2ludml0cm9kYl90YWJsZQAEAAkAAAAPaW52aXRyb2RiX2ZpZWxk
+ AAQACQAAAAtkZXNjcmlwdGlvbgAABAIAAAABAAQACQAAAAVuYW1lcwAAABAAAAADAAQACQAA
+ AA9pbnZpdHJvZGJfdGFibGUABAAJAAAAD2ludml0cm9kYl9maWVsZAAEAAkAAAALZGVzY3Jp
+ cHRpb24AAAD+
diff --git a/tests/testthat/test-tcplDefine.R b/tests/testthat/test-tcplDefine.R
index 7eca6e6d..e1c24166 100644
--- a/tests/testthat/test-tcplDefine.R
+++ b/tests/testthat/test-tcplDefine.R
@@ -1,24 +1,24 @@
test_that("empty returns full dictionary", {
tcplConf(drvr = "example")
- expect_snapshot(tcplDefine())
+ expect_snapshot_value(tcplDefine(), style = "serialize")
})
test_that("multiple values returns all necessary definitions", {
tcplConf(drvr = "example")
# just tables
- expect_snapshot(tcplDefine(c("chemical", "sample")))
+ expect_snapshot_value(tcplDefine(c("chemical", "sample")), style = "serialize")
# just fields
- expect_snapshot(tcplDefine(c("spid", "rval", "wllt")))
+ expect_snapshot_value(tcplDefine(c("spid", "rval", "wllt")), style = "serialize")
# mix of tables and fields
- expect_snapshot(tcplDefine(c("sc0", "chid")))
+ expect_snapshot_value(tcplDefine(c("sc0", "chid")), style = "serialize")
})
test_that("one value returns all necessary definitions", {
tcplConf(drvr = "example")
# just a table
- expect_snapshot(tcplDefine("chemical"))
+ expect_snapshot_value(tcplDefine("chemical"), style = "serialize")
# just a field
- expect_snapshot(tcplDefine("spid"))
+ expect_snapshot_value(tcplDefine("spid"), style = "serialize")
})
test_that("no values found shows a warning", {
diff --git a/vignettes/Data_retrieval.Rmd b/vignettes/Data_retrieval.Rmd
index 281d9959..934c408d 100644
--- a/vignettes/Data_retrieval.Rmd
+++ b/vignettes/Data_retrieval.Rmd
@@ -130,6 +130,32 @@ head(mc2_fmtd)
When loading data, the user must indicate the applicable fields and ids for the corresponding data level of interest. Loading level 0 (SC0 and MC0), MC1, and MC2 data the assay component id ($\mathit{acid}$) will always be used. As described in Table 1 of the tcpl Data Processing vignette, SC1 and MC3 processing levels perform data normalization where assay component ids ($\mathit{acid}$) are converted to assay endpoint ids ($\mathit{aeid}$). Thus, the SC1 and MC3 data tables contain both $\mathit{acid}$ and ($\mathit{aeid}$) ID's. Data can be loaded using either id as long as it is properly specified. Loading SC2, MC4, and MC5, one should always use the assay endpoint id ($\mathit{aeid}$). Selected id(s) are based on the primary key within each table containing data. Examples of loading data are detailed in later sections.
+### Assay Annotations
+
+Assay source, assay, assay component, and assay endpoint are registered via tcpl scripting into a collection of tables. The database structure takes the annotations and organizes them as attributes of the assay conductors, the assays (i.e., experiments), the assay components (i.e., raw readouts), or the assay endpoints (i.e., normalized component data) enabling aggregation and differentiation of the data generated through ToxCast and Tox21. The annotations capture four types of information:
+
+i. Identification information
+ii. Design information such as the technology, format, and objective aspects that decompress the assay’s innovations,
+iii. Target information such as the target of technological measurement and the
+biologically intended target, and
+iv. Analysis information about how the data were processed and analyzed.
+
+```{r annotation_query_ex, eval = FALSE}
+#load libraries and connections
+library(RMySQL)
+con <- dbConnect(drv = RMySQL::MySQL(), user="user", pass="pass", db="InvitroDB", host="host")
+#query database using RMySQL:
+#use source table to identify which ids are needed in subsequent queries.
+tcplLoadAsid()
+source <- tcplLoadAeid(fld="asid", val=1, add.fld = c("aid", "anm", "acid", "acnm"))
+#select annotation and subset by ids or name
+assay <- dbGetQuery(con, "SELECT * FROM invitrodb.assay where aid=1;")
+component <- dbGetQuery(con, "SELECT * FROM invitrodb.assay_component;")
+component <- subset(component, acid %in% source$acid)
+endpoint <- dbGetQuery(con, "SELECT * FROM invitrodb.assay_component_endpoint;")
+endpoint <- endpoint[grepl("ATG", endpoint$assay_component_endpoint_name),]
+```
+
### Chemical Information
The tcplLoadChem function returns chemical information for user specified parameters, e.g. the chemical name (chnm) and chemical id (chid). The tcplLoadClib function provides more information about the ToxCast chemical library used for sample generation.