Distant Reader

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 from a curated subset of CORD, a collection of more than 100,000 scholarly journal articles surrounding the topic of COVID-19. This resulted in a set of 786 item(s). The original versions of these items have been saved in a cache, and each of them have been transformed & saved as 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 website is a more verbose version of the narrative 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.

Provenance

This study carrel was originally named cord-2018-2019. It was created on 2020-11-28 at 13:41 by emorgan@nd.edu. The following query, applied against the local copy of our CORD database, was ( ( * NOT ( pdf_json:nan ) ) OR ( * NOT ( pmc_json:nan ) ) ) AND (year:"2019" OR year:"2018") .

Size & Scope

Your study carrel is 4,792,883 words long. Each item in your study carrel is, on average, 6,450 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 illustrate the overall size of your study carrel.

Readability

On a scale from 0 to 100, where 0 is very difficult and 100 is very easy, your documents have an average readability score of 47. 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 illustrate the overall readability of your study carrel.

Word Frequencies

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

virus, patients, cells, infection, study, cell, using, disease, viral, also, protein, human, used, respiratory, influenza, data, results, viruses, may, based, health, two, one, analysis, time, i, treatment, clinical, associated, studies, high, however, rna, control, group, different, use, risk, specific, immune, infections, cases, well, infected, response, patient, activity, expression, performed, first

Using the three most frequent words, the three files containing all of those words the most are: 1) 2018 ASPHO ABSTRACTS, 2) Scientific Session of the 16th World Congress of Endoscopic Surgery, Jointly Hosted by Society of American Gastrointestinal and Endoscopic Surgeons (SAGES) & Canadian Association of General Surgeons (CAGS), Seattle, Washington, USA, 11–14 April 2018: Poster Abstracts, and 3) 27th International Congress of the European Association for Endoscopic Surgery (EAES) Sevilla, Spain, 12–15 June 2019.

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

respiratory syndrome, influenza virus, infectious diseases, public health, virus infection, acute respiratory, immune response, respiratory tract, middle east, united states, east respiratory, immune responses, cord uid, doc id, syndrome coronavirus, risk factors, infectious disease, zika virus, respiratory syncytial, respiratory viruses, amino acid, syncytial virus, ebola virus, type i, saudi arabia, gene expression, viral infection, innate immune, cell lines, porcine epidemic, severe acute, bone marrow, viral infections, viral rna, immune system, infected cells, rna viruses, epidemic diarrhea, intensive care, systematic review, cell culture, diarrhea virus, performed using, avian influenza, nucleic acid, present study, statistically significant, epithelial cells, viral replication, cell line

And the three file that use all of the three most frequent phrases are: 1) Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement, 2) Detection Methods of Human and Animal Influenza Virus—Current Trends, and 3) Middle East respiratory syndrome: what we learned from the 2015 outbreak in the Republic of Korea.

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 your study carrel include:

rna, virus, patient, cell, mers, infection, dna, respiratory, disease, health, pcr, ebola, pedv, china, rsv, influenza, ifn, vaccine, protein, sars, hiv, icu, gene, zikv, zika, study, ibv, hcv, east, human, hiv-1, viral, usa, hbv, h1n1, elisa, ebov, chinese, bat, animal, united, supplementary, risk, model, middle, hospital, evd, die, cmv, cap

And now word clouds really begin to shine:

Topic Modeling

Topic modeling is another popular approach to connoting the aboutness of a corpus. If your study carrel could be summed up in a single word, then that word might be virus, and RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence is most about that word.

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

If your 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:

cells, virus, cell - Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation
health, patients, data - Health System in China
virus, influenza, respiratory - Simultaneous outbreaks of respiratory disease in wild chimpanzees caused by distinct viruses of human origin
patients, treatment, study - What the Intensivists Need to Know About Critically Ill Myeloma Patients
chitosan, protein, binding - Onkologie

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, patients, cells, infection, study, cell, disease, protein, data, results, viruses, influenza, time, analysis, treatment, studies, health, cases, risk, group, infections, activity, response, control, expression, use, gene, vaccine, proteins, number, detection, system, model, years, case, mice, patient, diseases, days, type, samples, children, host, role, levels, methods, blood, development, age, cancer

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, including, based, associated, increased, reported, perform, following, identified, found, compared, induced, developed, provided, detected, infected, caused, reduced, suggested, required, described, observed, determine, binding, indicating, treated, leaded, considered, relate, demonstrated, presented, resulting, contain, occurs, making, evaluated, improve, obtained, known, reveals, remains, given, involved, mediate, tested, targeted, affect, collect, assessed

Proper Nouns

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

Fig, RNA, MERS, PCR, China, CoV, C, T, Health, PEDV, IFN, A, Table, B, Ebola, S, SARS, HIV, USA, RSV, RT, II, United, mg, HBV, East, ZIKV, IBV, States, University, DNA, CD4, HCV, Zika, Middle, M, •, N, HIV-1, PBS, H1N1, mRNA, Africa, ELISA, Influenza, HA, der, ICU, L, S1

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, our, its, they, i, them, he, his, she, her, us, you, itself, one, themselves, your, my, me, him, nsp15, isgf3, u, s, yourself, ns3/4a, mrnas, imagej, ifitm3, herself, ourselves, ours, il-4rα, itims, himself, d509, irbcs, hifnα, 's, z004, t98hr, oneself, o139, nsp11, myself, mtorc1, interleukin-15, influenzavirusa, hlj-073

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, respiratory, human, clinical, high, different, specific, immune, positive, significant, infectious, acute, new, non, severe, higher, low, first, anti, important, similar, many, several, antiviral, laparoscopic, lower, molecular, common, early, single, negative, multiple, large, small, primary, potential, available, effective, genetic, bacterial, surgical, present, total, major, novel, possible, public, like, previous, recent

also, however, well, significantly, respectively, therefore, previously, highly, even, often, still, first, furthermore, especially, recently, moreover, directly, prior, currently, approximately, less, particularly, finally, usually, together, mainly, additionally, subsequently, now, potentially, relatively, commonly, specifically, frequently, generally, later, rather, statistically, widely, similarly, least, rapidly, indeed, much, successfully, likely, almost, alone, interestingly, yet

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.

Study carrel