Distant Reader - keyword-golgi-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 2021-05-24 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:golgi. 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 65 item(s) in this carrel, and this carrel is 521,868 words long. Each item in your study carrel is, on average, 9,155 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 48. 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:

golgi, protein, proteins, cells, membrane, cell, er, virus, also, transport, secretory, complex, arf, domain, i, vesicles, may, viral, pathway, membranes, surface, two, apparatus, formation, sorting, shown, localization, replication, tgn, structure, signal, type, linked, studies, cytoplasmic, one, however, plasma, role, compartment, lipid, receptor, transmembrane, specific, function, ii, amino, binding, coronavirus, containing

Using the three most frequent words, the three files containing all of those words the most are Golgi Structure and Function in Health, Stress, and Diseases, Molecular Interactions in the Assembly of Coronaviruses, and A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication.

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

golgi apparatus, plasma membrane, endoplasmic reticulum, golgi complex, cell surface, secretory pathway, membrane proteins, golgi network, membrane protein, amino acid, amino acids, secretory proteins, infected cells, golgi membranes, transmembrane domain, cytoplasmic domain, golgi cisternae, golgi localization, secretory granules, cytoplasmic tail, linked oligosaccharides, golgi stack, newly synthesized, mouse hepatitis, golgi retention, hepatitis virus, intermediate compartment, golgi transport, membrane traffic, mammalian cells, golgi compartment, golgi membrane, hela cells, epithelial cells, integral membrane, golgi stacks, vesicular stomatitis, vaccinia virus, sialic acid, intracellular transport, protein transport, coated vesicles, fusion proteins, stomatitis virus, rna replication, spanning domain, guanine nucleotide, nucleotide exchange, mdck cells, viral proteins

And the three file that use all of the three most frequent phrases are Cell Biology of Membrane Trafficking in Human Disease Membrane traffic in the secretory pathway: Take the ’A’ train: on fast tracks to the cell surface, and Golgi Structure and Function in Health, Stress, and Diseases.

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:

golgi, protein, cell, tgn, membrane, bfa, rna, mhv, arf1, secretory, sars, vsv, virus, vesicle, transport, oligosaccharide, man, inhibitor, glycoprotein, dppiv, dpap, copi, arf6, arf, wpb, wang, vwf, viral, tube, transporter, tmd, tgn38, tay, sy2, structure, snare, signal, section, sec7, sec, sds, scv, salmonella, s33d, s10, rsv, ros, rhodopsin, rer, replication

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 golgi, and Biological Function and Application of Picornaviral 2B Protein: A New Target for Antiviral Drug Development 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:

golgi, cells, protein - Membrane protein sorting in the yeast secretory pathway: evidence that the vacuole may be the default compartment
protein, proteins, membrane - The Use of Glycosylation Inhibitors to Study Glycoconjugate Function
golgi, protein, virus - A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication
membrane, golgi, proteins - Derivatives of activated H-ras lacking C-terminal lipid modifications retain transforming ability if targeted to the correct subcellular location
membrane, golgi, autophagy - Assembly of the silk fibroin elementary unit in endoplasmic reticulum and a role of L‐chain for protection of α1,2‐mannose residues in N‐linked oligosaccharide chains of fibrohexamerin/P25

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?":

protein, proteins, cells, membrane, cell, virus, transport, domain, vesicles, pathway, membranes, apparatus, surface, formation, complex, localization, replication, structure, type, studies, plasma, signal, role, compartment, receptor, lipid, sorting, residues, sequence, coronavirus, activity, acid, gene, fusion, retention, reticulum, infection, transmembrane, enzymes, structures, yeast, endoplasmic, function, region, glycoprotein, results, presence, domains, expression, addition

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:

show, contains, using, bound, require, suggest, involved, associated, linked, found, forms, indicate, occur, targeting, induced, inhibit, see, expressed, appears, mediated, described, regulating, localized, determining, results, observe, includes, following, causes, labeled, demonstrate, budding, known, provide, sorted, identify, interacting, affected, infected, treated, synthesized, encodes, lead, detect, blocked, produced, increasing, remains, incubated, reduced

Proper Nouns

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

Golgi, ER, Fig, M, TGN, BFA, A, trans, RNA, MHV, II, C, S, N, cis, COPI, GA, DPAP, pH, SARS, IC, G, cisternae, B, VSV, Arf, GlcNAc, Kexlp, ras, monensin, SDS, Kre2p, H, A59, ALP, ARF1, GBF1, Arf1, K, PBS, vacuolar, HeLa, D, CoV, GTPase, IBV, COPII, GTP, ARF, Ii

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?"

it, their, its, we, they, i, our, them, itself, us, one, themselves, his, he, her, grasp55, me, rab8, p450s, my, earlier\, tgn38, tbarf1, s, kre2p, your, tr]mt, s189, rab1b, ptdlns(4,5)p2, pp38-gfp, pmt3p, pis]methionine, p58, oneself, ofisgs, mrnas, mannose\, log1, k(x)kxx, ile8, il-1β, i"i20, hapg5p, gln37?ile, gate16, di(c24:)pc, connexin-26, clear^it, c16:0,c18:1)pc

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?"

secretory, viral, cytoplasmic, specific, different, intracellular, human, cellular, similar, complex, structural, present, small, vesicular, molecular, dependent, large, early, several, high, important, distinct, anti, many, lysosomal, mutant, functional, mammalian, hydrophobic, first, single, major, like, non, soluble, intermediate, various, normal, new, possible, late, epithelial, wild, essential, low, active, sensitive, infected, apical, polarized

also, however, well, therefore, previously, respectively, highly, newly, still, even, rather, interestingly, directly, probably, furthermore, recently, together, first, specifically, normally, rapidly, yet, often, now, indeed, presumably, completely, similarly, finally, much, clearly, subsequently, less, relatively, perhaps, already, later, functionally, moreover, partially, back, strongly, least, significantly, immediately, apparently, approximately, prior, possibly, generally

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.

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