Distant Reader - keyword-rna-cord

Introduction

This is a Distant Reader "study carrel", a set of structured data intended to help the student, researcher, or scholar use & understand a corpus.

This study carrel was created on 2021-05-25 by Eric Morgan <emorgan@nd.edu>. The carrel was created using the Distant Reader cord process, and the input was the result of a query applied to a local mirror of CORD, a data set of scholarly articles on the topic of COVID-19. The actual query was: keywords:rna. The results of this query were saved in a cache and transformed into a set of plain text files. All of the analysis -- "reading" -- has been done against these plain text files. For example, a short narrative report has been created. This Web page is a more verbose version of that report.

All study carrels are self-contained -- no Internet connection is necessary to use them. Download this carrel for offline reading. The carrel is made up of many subdirectories and data files. The manifest describes each one in greater detail.

Size

There are 1,349 item(s) in this carrel, and this carrel is 11,763,802 words long. Each item in your study carrel is, on average, 8,911 words long. If you dig deeper, then you might want to save yourself some time by reading a shorter item. On the other hand, if your desire is for more detail, then you might consider reading a longer item. The following charts illustrate the overall size of the carrel.

Readability

On a scale from 0 to 100, where 0 is very difficult and 100 is very easy, the documents have an average readability score of 49. Consequently, if you want to read something more simplistic, then consider a document with a higher score. If you want something more specialized, then consider something with a lower score. The following charts illustrate the overall readability of the carrel.

Word Frequencies

By merely counting & tabulating the frequency of individual words or phrases, you can begin to get an understanding of the carrel's "aboutness". Excluding "stop words", some of the more frequent words include:

rna, virus, cells, viral, protein, cell, viruses, using, infection, also, proteins, sars, cov, human, replication, expression, gene, patients, i, used, dna, two, study, may, results, analysis, sequence, genome, coronavirus, specific, host, activity, binding, infected, different, one, based, blood, data, disease, samples, structure, mrna, pcr, high, however, type, genes, studies, associated

Using the three most frequent words, the three files containing all of those words the most are Oral and Poster Manuscripts, Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed, and The Molecular Biology of Coronaviruses.

The most frequent two-word phrases (bigrams) include:

viral rna, rna viruses, respiratory syndrome, infected cells, gene expression, rna polymerase, acute respiratory, nucleic acid, virus infection, virus replication, viral replication, severe acute, amino acid, influenza virus, rna synthesis, immune response, type i, syndrome coronavirus, innate immune, rna replication, stranded rna, rna virus, dependent rna, strand rna, genomic rna, cell culture, cell lines, host cell, viral genome, immune responses, viral infection, amino acids, nucleic acids, novel coronavirus, viral proteins, doc id, cord uid, virus rna, antiviral activity, reverse transcription, secondary structure, hepatitis virus, rna interference, cell line, viral load, structural proteins, dengue virus, virus type, immune system, nucleocapsid protein

And the three file that use all of the three most frequent phrases are Origins and Evolution of the Global RNA Virome Rna Viruses Redirect Host Factors to Better Amplify Their Genome, and Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell.

While often deemed superficial or sophomoric, rudimentary frequencies and their associated "word clouds" can be quite insightful:

Keywords

Sets of keywords -- statistically significant words -- can be enumerated by comparing the relative frequency of words with the number of times the words appear in an entire corpus. Some of the most statistically significant keywords in the carrel include:

rna, sars, virus, dna, pcr, cell, protein, ifn, covid-19, hcv, viral, gene, hiv-1, cov-2, mhv, patient, infection, mers, rig, sequence, hiv, study, structure, human, ibv, ace2, hbv, china, result, expression, university, sirna, prrsv, genome, disease, vero, target, coronavirus, bat, atp, sample, orf, method, lamp, delivery, vaccine, rsv, replication, mutation, chikv

And now word clouds really begin to shine:

Topic Modeling

Topic modeling is another popular approach to connoting the aboutness of a corpus. If the study carrel could be summed up in a single word, then that word might be rna, and Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics is most about that word.

If the study carrel could be summed up in three words ("topics") then those words and their significantly associated titles include:

If the study carrel could be summed up in five topics, and each topic were each denoted with three words, then those topics and their most significantly associated files would be:

rna, virus, protein - Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery
virus, rna, viruses - Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus
cov, sars, blood - KAPITEL 13 Infektionskrankheiten
cells, cell, patients - Scientific Abstracts
protein, cells, cell - 1 Micro-organismen, de mens en het ontstaan van infectieziekten: algemene principes

Moreover, the totality of the study carrel's aboutness, can be visualized with the following pie chart:

Noun & Verbs

Through an analysis of your study carrel's parts-of-speech, you are able to answer question beyonds aboutness. For example, a list of the most frequent nouns helps you answer what questions; "What is discussed in this collection?":

virus, cells, protein, cell, viruses, infection, proteins, replication, expression, patients, gene, results, sequence, study, analysis, genome, host, activity, dna, blood, data, samples, coronavirus, disease, structure, genes, studies, type, time, sequences, treatment, detection, response, role, system, levels, influenza, acid, transcription, control, group, number, membrane, methods, translation, rnas, synthesis, effect, site, polymerase

An enumeration of the verbs helps you learn what actions take place in a text or what the things in the text do. Very frequently, the most common lemmatized verbs are "be", "have", and "do"; the more interesting verbs usually occur further down the list of frequencies:

used, showed, binding, including, based, induce, contains, identifying, found, infected, associated, suggests, increasing, detect, comparing, follows, observed, determining, require, performed, indicate, provides, reported, expressed, involved, targeting, inhibit, mediating, described, causing, resulting, reveal, known, demonstrated, reduced, led, develop, obtained, produced, encoded, generates, test, occurs, regulate, form, treated, derive, allowed, made, relates

Proper Nouns

An extraction of proper nouns helps you determine the names of people and places in your study carrel.

RNA, SARS, CoV-2, Fig, PCR, C, HCV, IFN, CoV, RT, mRNA, T, M, DNA, COVID-19, siRNA, HIV-1, A, N, B, S, HIV, MHV, II, University, Table, L, HBV, USA, RdRp, MERS, ⁄, miRNA, G, miRNAs, Coronavirus, China, mg, Figure, I, IBV, D, siRNAs, RNase, Virus, ORF, pH, E., ACE2, K

An analysis of personal pronouns enables you to answer at least two questions: 1) "What, if any, is the overall gender of my study carrel?", and 2) "To what degree are the texts in my study carrel self-centered versus inclusive?"

we, it, their, its, our, i, they, them, us, his, itself, he, one, her, she, themselves, you, your, mrnas, my, nsp15, nsp10, me, him, ourselves, ns3/4a, imagej, himself, nsp7, iosns, isg20, mg, s, ifit5, 2h5-a14, nsp1, isgf3, p~, ours, eef1a, u, pdcs, p210bcr, em, rss1gfp, rad5, nsps, irfibv32, ifit1, herself

Below are words cloud of your study carrel's proper & personal pronouns.

Adjectives & Verbs

Learning about a corpus's adjectives and adverbs helps you answer how questions: "How are things described and how are things done?" An analysis of adjectives and adverbs also points to a corpus's overall sentiment. "In general, is my study carrel positive or negative?"

viral, human, specific, different, high, antiviral, clinical, respiratory, positive, immune, cellular, non, new, molecular, anti, several, single, structural, important, small, similar, dependent, negative, first, many, low, severe, significant, like, novel, infectious, acute, higher, present, large, genetic, potential, multiple, genomic, possible, infected, functional, major, nucleic, available, early, common, various, recent, active

also, however, well, highly, respectively, therefore, previously, significantly, recently, even, still, directly, furthermore, moreover, together, first, currently, often, approximately, interestingly, specifically, nt, less, especially, now, double, finally, yet, rather, prior, relatively, subsequently, mainly, particularly, indeed, much, similarly, additionally, generally, likely, potentially, rapidly, far, usually, probably, later, strongly, single, efficiently, fully

Next steps

There is much more to a study carrel than the things outlined above. Use this page's menubar to navigate and explore in more detail. There you will find additional features & functions including: ngrams, parts-of-speech, grammars, named entities, topic modeling, a simple search interface, etc.

Again, study carrels are self-contained. Download this carrel for offline viewing and use.

Thank you for using the Distant Reader.