Distant Reader - journal-biorxiv-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 2021-05-30 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: facet_journal:"bioRxiv". 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 701 item(s) in this carrel, and this carrel is 2,524,922 words long. Each item in your study carrel is, on average, 3,970 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 52. 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:

sars, cov, cells, protein, cell, using, virus, data, human, viral, covid, analysis, coronavirus, ace, also, infection, binding, used, rna, two, based, expression, i, proteins, spike, high, structure, one, study, sequence, different, may, disease, receptor, gene, model, samples, sequences, rbd, results, genes, time, specific, genome, host, table, patients, single, well, number

Using the three most frequent words, the three files containing all of those words the most are COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms, A zebrafish model for COVID-19 recapitulates olfactory and cardiovascular pathophysiologies caused by SARS-CoV-2, and Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells.

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

spike protein, respiratory syndrome, acute respiratory, severe acute, syndrome coronavirus, novel coronavirus, amino acid, cord uid, doc id, biorxiv doi, gene expression, cell types, immune response, epithelial cells, coronavirus disease, sars coronavirus, receptor binding, binding domain, spike glycoprotein, performed using, neutralizing antibodies, viral rna, viral replication, host cell, human ace, infected cells, converting enzyme, type i, room temperature, virus infection, immune responses, viral infection, amino acids, supplementary table, innate immune, cell entry, binding affinity, extended data, coronavirus spike, severe covid, viral genome, ace receptor, molecular dynamics, crystal structure, previously described, single cell, rna viruses, cell lines, ace expression, cell type

And the three file that use all of the three most frequent phrases are When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses Highly potent bispecific sybodies neutralize SARS-CoV-2, and Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate.

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:

sars, rna, ace2, cov-2, cell, rbd, covid-19, protein, dna, pcr, supplementary, spike, sequence, virus, tmprss2, hla, gene, structure, mutation, mers, ifn, drug, data, antibody, vero, disease, cd8, mouse, d614, cd4, bat, variant, vaccine, tms, site, sample, human, elisa, eeg, crispr, coronavirus, zikv, usa, time, table, sequencing, selection, receptor, read, pro

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 sars, and Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex 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:

sars, cov, protein - Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM
sars, cov, data - Neurophysiological Correlates of the Dunning-Kruger Effect
rna, cells, using - Structural and molecular basis for protein-stimulated ribosomal frameshifting in Theiler’s murine encephalomyelitis virus
mice, sars, infection - Selective Nanotherapeutic Targeting of the Neutrophil Subset Mediating Inflammatory Injury
cells, cell, virus - Taxonomic revision of the threatened African genus Pseudohydrosme Engl. (Araceae), with P. ebo, a new, Critically Endangered species from Ebo, Cameroon

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?":

cells, protein, cell, virus, data, analysis, infection, expression, proteins, coronavirus, sequence, sequences, structure, samples, study, model, receptor, results, time, spike, genes, patients, gene, genome, number, disease, host, response, mice, mutations, antibody, studies, activity, antibodies, type, viruses, control, system, residues, site, lung, domain, acid, levels, replication, treatment, binding, mutation, detection, drug

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:

using, shown, bound, based, identify, including, found, performed, compare, suggested, observe, followed, indicate, provide, increasing, containing, associated, revealed, induces, reported, expressed, predict, detect, determine, generated, describe, saw, tested, infected, obtained, reduced, cause, resulting, given, known, represents, developing, targeting, allowing, demonstrate, related, making, required, mediated, lead, analyzed, considered, neutralize, treated, added

Proper Nouns

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

SARS, CoV-2, Fig, RNA, ACE2, COVID-19, T, S, RBD, CoV, C, Table, S1, Figure, PCR, Coronavirus, S2, Supplementary, N, MERS, M, China, RT, G, TMPRSS2, Human, Spike, DOI, Vero, sha, A, B, Protein, IFN, Data, Wuhan, PBS, CD8, F, K, II, Virus, ±, HLA, pH, CD4, L, D, USA, Disease

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, our, their, its, they, i, them, us, his, itself, one, themselves, he, you, your, my, her, she, me, imagej, em, ourselves, hao, si3n4, s, igg1, cbae-1, u, rrbd-15, ours, nlrp12, mine, iosns, il-1β, directms1, ıt, y-27632, usa_wa1/2020, rad5, nsp7, mrnas, l452, l270, ippa17-a04, igfbp2, https://github.com/ababaian/serratus, hace2, fncas9, etn

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, high, different, specific, immune, single, respiratory, severe, non, positive, similar, clinical, low, new, higher, first, molecular, structural, multiple, acute, novel, potential, significant, large, available, antiviral, anti, several, many, covid-19, small, key, possible, negative, functional, important, lower, present, cellular, like, dependent, inflammatory, full, genomic, total, previous, global, infected, consistent

also, however, well, respectively, highly, therefore, previously, significantly, even, first, together, directly, finally, recently, furthermore, still, next, less, interestingly, specifically, relatively, moreover, currently, prior, additionally, potentially, especially, much, likely, often, rather, indeed, rapidly, notably, least, particularly, approximately, strongly, similarly, already, fully, hence, now, importantly, closely, differentially, instead, clearly, subsequently, widely

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.