Contents

1 Introduction

Metadata are crucial to all forms of statistical analysis. Metadata are used to define formal steps of upstream data preprocessing, to annotate outcomes and covariates, and to interpret inferential results.

The ssrch package was developed to provide a lightweight approach to searching a metadata corpus with R. There are three basic steps:

We illustrate the system using a collection of tables of metadata about cancer transcriptomics.

2 Illustration

To provide a sense of what is at stake, we work with 68 CSV files derived from the NCBI Sequence Read Archive metadata.
The files consist of contents of the sample.attribute subtable of study metadata retrieved using the SRAdbV2 package at github.com:seandavi/SRAdbV2. The CSV files are lodged in a zip file canc68.zip with the ssrch package in inst/cancer_corpus.

The CSV files have been indexed in an S4 object of class DocSet.

data(docset_cancer68)
docset_cancer68
## ssrch DocSet resource:
##  68 documents, 9934 records
## some titles:
##   Single cell analysis of lung adenocarcinoma cell lines ... (DRP001358)
##   Single cell analysis of lung adenocarcinoma cell lines ... (DRP002586)
##   Integrative systematic analyses of mutational and trans... (ERP010142)
##   Identification_and_molecular_charaterization_of_new_tum... (ERP012527)
##   Whole transcriptome profiling of Esophageal adenocarcin... (ERP013206)
##   Transcriptional landscape of human tissue lymphocytes u... (ERP013260)

A single document can be retrieved with the retrieve_doc function, given the study accession number.

retrieve_doc("ERP010142", docset_cancer68)[1:3,1:5]
##   X study.accession experiment.accession    Bcl.2 Colletion.date
## 1 1       ERP010142            ERX943467 Negative     2001-10-10
## 2 2       ERP010142            ERX943327 Positive     2005-12-23
## 3 3       ERP010142            ERX943378 Negative     2001-07-11

2.1 Diversity of field names

There is partial standardization of field names in this corpus, but there is considerable variation among studies in the number and types of fields used.

docids = ls(envir=docs2kw(docset_cancer68))
allc = lapply(docids, 
   function(x) try(retrieve_doc(x, docset_cancer68)))
summary(sapply(allc,ncol))
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   4.000   6.000   8.000   9.221  10.000  25.000
lapply(allc[c(11,55)], names)
## [[1]]
##  [1] "X"                     "study.accession"       "experiment.accession" 
##  [4] "source_name"           "tissue"                "tissue.archive.method"
##  [7] "cell.line"             "cell.type"             "development.stage"    
## [10] "disease.status"       
## 
## [[2]]
## [1] "X"                    "study.accession"      "experiment.accession"
## [4] "source_name"          "tissue"               "cell.type"           
## [7] "cell.activation"      "cell.category"        "barcode"

The ssrch package provides tools for identifying studies in which a given field is used, and in which given values are recorded.

A motivating example is determining what studies involve measurements on normal tissue adjacent to tumor. In our collection, this can be assessed via:

library(ssrch)
searchDocs("Adjacent", docset_cancer68, ignore.case=TRUE)
##                     hits      docs
## 1               Adjacent SRP056696
## 2               Adjacent SRP111343
## 3 Adjacent Normal tissue SRP056696
## 4        Adjacent normal SRP111343
## 5               adjacent SRP069212
## 6               adjacent SRP073447
## 7        adjacent normal SRP069212
## 8        adjacent normal SRP073447
## 9        benign_adjacent SRP011439

2.2 Managing tokenized metadata

Before getting into the details of search engine construction, we review some high-level concepts and methods.

First, we have the container for managing our search resource.

getClass(class(docset_cancer68))
## Class "DocSet" [package "ssrch"]
## 
## Slots:
##                                                                             
## Name:        kw2docs     docs2recs       docs2kw        titles          urls
## Class:   environment   environment   environment     character     character
##                     
## Name:  doc_retriever
## Class:      function

docset_cancer68 is the result of using the ssrch function parseDoc in conjunction with the CSV files zipped in ssrch/inst/cancer_corpus. It is an S4 class instance that manages environments mapping from keywords to documents, documents to records, documents to keywords,

Furthermore, DocSet instances can have a component that retrieves parsed documents from the corpus.

2.3 Querying the corpus

We’ll search for the phrase Non Small Cell with an optional hyphen, ignoring character case of possible hits, including as well the abbreviation for Non-small cell lung cancer.

NSChits = searchDocs("Non.Small Cell|NSCLC$", docset_cancer68, ignore.case=TRUE)
NSChits
##                                 hits      docs
## 1                              NSCLC SRP093349
## 2         Non Small Cell Lung Cancer ERP013260
## 3 Non-Small Cell Lung Cancer (NSCLC) SRP107198

Three studies, three different patterns matched by the query string. We can use retrieve_doc to look at the contents of the metadata tables for these studies.

NSCdocs = lapply(unique(NSChits$docs), 
   function(x) retrieve_doc(x, docset_cancer68))
names(NSCdocs) = NSChits$docs
datatable(NSCdocs[[1]], options=list(lengthMenu=c(3,5,10)))
datatable(NSCdocs[[2]], options=list(lengthMenu=c(3,5,10)))
datatable(NSCdocs[[3]], options=list(lengthMenu=c(3,5,10)))

3 A prototypical app

The ctxsearch function starts a shiny app that provides access to full attribute data via a selectize input that uses all tokens in the corpus (filtered).

ctxsearch illustration

4 Further work

The tab set should be prunable.

This will be the basis of an interactive interface to the human transcriptome compendium