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Cloud of Science. 2020. T. 7. № 1
http://cloudofscience.ru
Formats of Scientific e-Documents in the Modern
Information-Communication Space
T. V. Busygina, V. V. Rykova
Scientific Bibliography of the State Public Scientific-Technological Library
of the Siberian Branch of the Russian Academy of Sciences
st. Voshod, 15, Novosibirsk, Russia, 630200
e-mail: busygina @spsl.nsc.ru, rykova @spsl.nsc.ru
Abstract. The article discusses the problem of an electronic scientific document
existence in the electronic environment. The study objective is to overview
document formats (HTML, PDF, CDF), shows their advantages and disadvantages. The paper describes 1) widely used formats: HTML (Hyper-Text
Markup Language) and PDF (Portable Document Format); 2) characterizes the
format of future — CDF (Computable Document Format); formats of data descriptions (in particular, scientific) on the Resource Description Framework
standard containing Linked Open Data. It takes advantages of a traditional
scientific document existence in e-form. They are the following: including text
and non-textual elements (3D images, sound); performing calculations and
make changes directly in a document file; hyperlinking to the Internet space,
or to other files located on a computer locally; creating open related scientific
data, discussing the document in e-science space in real time regime. An electronic scientific document is a modern means of scientific communication incorporated into the developing digital scientific infrastructure.
Keywords: scientific document, e-book formats, HyperText Markup Language
(HTML) format, Portable Document Format (PDF), Computable Document
Format (CDF).
1. Introduction
The electronic revolution in scientific communication is related to ideas about the ‘liberation from print’ and the explosive effects of electronic text [1]. Digital technologies affect
both the research practice, and representing its results. The necessity to visualize complex
data (e. g. data sets, genomic study, simulation, etc.) make specialists to transform and
improve old formats of scientific papers structuring their content, providing visual perception of digital information.
A scientific document is a form of communication by means of which it is customary to deliver portions of scientific information to members of the world professional scientific community. Scientific documents are material objects containing scientific information and intend for its storage and use in public practice. Like others objects they
should be classified according to their inherent characteristics.
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Formats of scientific e-documents in the modern
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Depending on the way of information presentation, the following types of documents
are distinguished:
1) text (books, magazines, reports, etc.);
2) graphic (drawings, diagrams, diagrams);
3) audiovisual (sound recordings, film and video films, CD- DVD-ROMs);
4) computer-readable (microfilms or electronic ones — on floppy disks or CDs), etc.
In addition, the documents are divided into primary documents (documents containing direct results of scientific research and development, new scientific information, facts,
ideas) and secondary ones, which are results of analytical-synthetic and logical processing of information or data contained in primary documents (annotations, abstracts,
reviews). Both primary and secondary documents are separated into published and unpublished ones. The ways to classify scientific documents are not limited to those listed
above. Altmetric developers propose to consider a wider range of objects (documents/products) as scientific products (term "a scientific document" is substituted with "a
scientific product"): presentations at scientific events, video lectures, software developments, etc. Altmetrics record the activity of scholars and scientists in the electronic environment, i. e. are metrics complementary to traditional ones [2].
2. Scientific publications’ formats
Computer technologies development promotes presenting all scientific documents electronically. It can already be argued that nowadays all scientific documents are initially
created in e-form, as computing has firmly entered our everyday life, and scholars have
become the first active users of it (strictly speaking, the computer technology progress
itself is the result of scientific achievements). This applies not only to text documents:
nowadays graph and drawing, audio-visual documents are created using computers as
well. Publishing houses have successfully mastered the computer texts layout. Electronic
publishing develops, and the types of scientific documents mentioned above might stay
only in an electronic form published as e-books, e-journals, placed into e-repositories, elibraries, full-text databases. Those scientific documents that existed only on paper bearers or photographic films should be changes into digital formats [3].
Scientific publications exist in almost all formats, in which e-books are represented [4]:
 plain text;
 text in HTML format, open format of Electronic Publication (.epub), OPF FlipBook, OpenDocument, SGML, XML, FictionBook (.fb2), TeX, PDF, Microsoft
HTMLHelp (.chm), eReader (.lit), PostScript (.ps, .eps), ExeBook, Mobipocket
(.prc), etc.;
 graphic bitmap formats — TIFF, JPEG, DjVu, etc .;
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 multimedia books — in addition to text and graphics contain files in the formats
SWF, EXE, audio, etc.; some software (FlipBook Maker, Flip PDF) allow converting e-books of some formats (doc, txt, pdf, html) into editions with the effect
of paging which can be accompanied by audio files of "rustling pages.");
 books in java-MIDlet format for mobile devices, such as cell phones with java
(J2ME) support, handheld personal computers;
 books in a form of applications for a specific operating system, including both its
content and a specialized software of file viewer, which prevents copying a book
and browsing it without a shell program.
Scientific e-documents being at local digital bearers and in the Internet have advantages and disadvantages.
3. HyperText Markup Language (HTML) format
T. Berners-Lee invented the web with HTML as a publishing language in 1989 [5] based
on the Standard Generalized Mark-up Language (SGML), an internationally agreed upon
method for marking up text into structural units such as paragraphs, headings, list items
etc. Publishing houses web sites present scientific documents in formats, which give users
opportunities to profit the whole complex of services possible only under functioning edocuments in the Internet. HTML format allows presenting drawings in the form of different size images, Microsoft PowerPoint presentations, tables in Comma Separated Values, Microsoft Excel, etc., which can be downloaded separately from the text of the article (Fig. 1).
All e-document formats, and in particular HTML-format, have a functional capability
of non-linear information reading based on internal and external hypertext links embedded in the document without leaving the initial text. Applying in-text hyperlinks users can
go to references, e-supplements, publishers' websites, full texts of the cited articles. The
articles’ full texts submitted to the SciFinder database (the platform presented the specialized chemical DB Chemical Abstracts) has hyperlinks from chemical formulas to the DB
of chemical compounds CAS Registry [6], Reaxys [7]. Such information is of great value
for chemists and biochemists. HTML files of DB Scopus provide the opportunity for specialists (physicians, geologists, etc.) to get other information products of Elsevier (PharmaPendium, Pathway Studio, Geofacets). E-supplements contain information, which can
not be included in the printed paper due to its large volume or other reasons (video, software, maps, etc.).
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Formats of scientific e-documents in the modern
information-communication space
Figure 1. The article in HTML-format can be represented as images of different sizes, as Microsoft PowerPoint presentations, tables — in csv (Microsoft Excel), etc., they can be downloaded
separately from the text of the article
In Web of Science and Scopus DBs, publisher sites, scholars’ networks scientific
documents presentation is accompanied by their scientometric and altmetric characteristics; it is possible to export automatically their bibliographic description (with metadata)
to bibliographic managers (EndNote, Mendeley, CiteULike, Zotero, etc.) to organize personal electronic libraries of scientists and to compile lists of references while creating a
scientific e-document.
In connection with the development of the digital scientific documentary infrastructure, there are Registry Agencies (CrossRef, DataCite) assuming the function to collect
information about digital objects. Information about the object (in particular a scientific edocument) is encrypted in the form of a digital object identifier (DOI), which is a unique
string of letters and numbers coding information about the publisher and the document
location in a virtual space. DOI is becoming an element of a bibliographic record in bibliographic DBs. The user can find e-documents with this identifier in the Internet open access or in a certain DB if there is a license access to it.
4. Portable Document Format (PDF)
The most widely used format for submitting scientific documents is the Portable Document Format (PDF). PDF since July 1, 2008 is an open standard maintained by the Inter-
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national Organization for Standardization (ISO) [8]. PDF is a cross-platform format for
e-documents developed by Adobe Systems using a number of PostScript features. PDF is
a file format used to present and exchange documents reliably, independent of software,
hardware, or operating system [9]. There are lots of software for viewing (free: MuPDF,
Evince, Okular, SumatraPDF, Mozilla Firefox; proprietary — Adobe Reader Foxit Reader, Google Chrome, PDF-XChange Viewer, PDFMaster, STDU Viewer). A significant
number of modern professional printing equipment has hardware support for PDF format,
which allows printing documents in this format without any software. The traditional way
of creating PDF documents is a virtual printer, that is, the document is formed in its specialized software — graphics or text editor, CAD, etc., and then exported to PDF for distribution in electronic form, transfer to the printing house and so on.
Initially this format was extremely unpopular:
 Adobe software for reading and creating PDF wasn’t free;
 there was no support for external links, which made it almost useless on the
World Wide Web;
 PDF documents were larger than conventional texts, which meant a longer download on slow modems widely used that time;
 feeble devices displayed PDF documents were with noticeable delays;
 there were several competing formats, such as Envoy, Common Ground Digital
Paper, Farallon Replica; even own PostScript was a competitor.
After releasing a free version of Acrobat Reader (later renamed Adobe Reader) to
read PDF documents by Adobe, the popularity of this format raised. PDF format has
changed in time, and continues evolving. New opportunities appear: passwords, links,
streams, device-independent color rendering, interactive elements, mouse event processing, multimedia types, Unicode, improved color and graphics representation, digital
signatures, ICC and DeviceN color spaces, JavaScript, JBIG2, transparency, text layer
OCR (optical character recognition), JPEG 2000, linked multimedia, object streams, cross
threads, layers, embedded multimedia, 3D, XML forms, AES-cipher AES encryption
with a 256-bit key, XFA 3.0). There are several format specifications expanding each
other consistently. A software new version is developed for each new specification in the
Adobe Acrobat package.
Scientific e-documents (books, articles, collections) in PDF can be printed (partially
or completely) on paper, read from a computer screen or a special portable device designed specifically for this purpose. However, reading from a computer screen is uncomfortable, despite the fact that PDF readers give an ability to scale documents (changing
the text position on a screen). Reading e-documents in PDF using any "e-book" device is
not quite comfortable, as it’s scaled poorly on it. In addition, if "e-book" supports the
technology of e-ink, e-paper graphic images appear in grayscale. The technology of mul-
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Busygina T. V.,
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Formats of scientific e-documents in the modern
information-communication space
ti-color (polychrome) paper is under development, but a common user it is still low accessible and have a number of disadvantages. In particular, e-ink color displays do not
have enough vibrant colors, color e-documents should be read at devices with LCD displays.
PDF format is the most prevalent in the scientific literature because it is a publishing
format, where books or articles appear in a print-ready form. In particular, the document
pages are numbered. This allows referring specific parts of the text, i. e. to cite the document. In scientometrics, the citation is regarded as an act and a technique of scientific
communication [10]. The text in FB2 and other formats is easily formatted, a user can
choose the font size for easy reading, but document content in this format can’t be cited,
as the number of pages varies depending on a user-selectable font. The citing text or image is placed in the text at different pages depending on the selected size.
For convenient reading of scientific documents some systems started to give an opportunity to view and download e-documents in various formats (Fig. 2): PDF (which can
be printed, cited), ePub format (PubMed Central) elaborated by the International Digital
Publishing Forum in 2007, which is more convenient to scale and read for eBooks.
Figure 2. Pubmed Central. In the upper right corner (red) are links to read (Epub Reader) and
download articles in ePub(beta), PDF
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5. Computable Document Format (CDF)
Nowadays PDF continues to be the most common format of scientific documents, but it
is simply a tracing-paper without representing a dynamic phenomena simulated by computing. New formats appear in response to challenges that arise before scientific publications [11]. In 2011, a private company Wolfram Research (led by Stephen Wolfram) introduced a new format for electronic documents called the Computable Document Format
(CDF) [12]. According to the developers, it is a more perfect format alternative to the
popular PDF, it is even called PDF "killer". According to the company, the offered format is more suitable for presenting data such as infographics, training aids, journal articles, various kinds of presentations and reports. Their text can include interactive elements, graphs, charts, diagrams, which contents might be controlled by users themselves.
For example, it is possible to rearrange the graph for other data; to add video or other media files making the information more visible and convenient. A special plug-in has been
developed that allows uploading a document to the browser window to view CDF-files,
which can be downloaded free from the official site. To create CDF files, the commercial
computer system Mathematica [13] of Wolfram Research is intended. Distribution of authored works for non-commercial use under the name FreeCDF is licensed under Creative
Commons Attribution-ShareAlike License (CC BY-SA) [14].
So, simple resumes and articles, for example, are still perfectly fine in PDF-format,
but interactive data and textbooks are better in CDF.
6. Semantic Web
Developers of the Semantic Web and open connected data concepts advocate for a different format of resources and scientific documents as a variety of resources.
The Semantic Web is an open global semantic web formed on the World Wide Web
basis by standardizing the presentation of information in a form suitable for machine processing. The notion "Semantic Web" was introduced first by Sir Tim Berners-Lee [15]
(inventor of the World Wide Web) in September 1998, who proposed the idea of related
data based on four principles stimulating the application of web basic principles to access
data:
 use of universal resource identifiers (URIs) as object names;
 using HTTP URI to implement the ability to access these names;
 providing useful information to anyone who accesses the URI using standards
(Resource Description Format (RDF), Protocol and RDF Query Language
(SPARQL);
 including links to other URIs that allow users to find additional information.
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Formats of scientific e-documents in the modern
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Linked Data are data sets published in RDF format using the Uniform Resource
Identifier (URI) to identify the elements they contain [16]. Linked Open Data are related
sets of data published in RDF format and suitable for use and re-release by users for their
own purposes without any restrictions in the form of copyrights, patents and other control
mechanisms [17].
A scientific document, database and other research resources should be organized in
such a way that they are a source of related open data. This implies a qualitatively different organization and functioning of information (scientific, in particular) based on modern information technologies. Open related scientific data creates e-Science space, where
the dominant role is played by scientific information and its processing.
The traditional book, before acquiring a modern form, went a long way of evolution
(from records on clay tablets, birch bark, on papyrus, cloth, leather etc.). The printed
book has now been formed: it is recognized in certain formats (sizes), characterized by
ergonomics, has the necessary set of information for its exhaustive bibliographic description (information about the author(s), publisher(s), places and years of publication, systematization codes. When creating a traditional book human aesthetic demands are realized in its design (cover, illustrations).
In the professional scientific community, the traditions to design research papers,
theses, dissertations, and others have been formed in a traditional paper medium. As concerning books (monographs), articles in e-forms, humanity is looking for forms of their
existence. Still scientific e-products are traditional documents translated into e-form.
However, developers propose formats, which will have the advantages of a scientific
document existence in an electronic form:
 an ability to include multimedia in a book, to calculate and make changes directly
in a paper file (CDF);
 a possibility to click hyperlinks and open files located locally on a computer or in
the Internet, to create linked scientific data and form e-Science space.
7. Summary
Thus, we can observe evolution of scientific e-documents formats. A true electronic document includes a text and non-textual elements, such as 3d images, sounds, animation
etc., i. e. the text will play a less prominent role in the future, while non-textual component come to the fore [18].
Changing touches not only in documents’ format, but scientific periodicals as well.
A new format of journals has recently appeared, e. g. “Videoscience” is the first Russian
journal of visual studies, which gives the opportunity maximal clear and full to demonstrate new research and developments in a research paper using video, provides distribution articles in YouTube and social networks, where scientific communication continue
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after the document has published in a real time regime [19]. It means that scientists could
shear their study results much wider and earlier to the academic community. Open science became a new culture of science as “scientists share results almost immediately and
with a very wide audience” [20].
Perhaps in the future, scientists will report the results of their research, not formalizing them in the form of traditional scientific documents, but only placing them on the
public's court in scientific social networks. For instance, the Mendeley system platform,
which is both a bibliographic manager and a scientific social network, after its acquisition
by Elsevier, has a section “Datasets”, where it’s proposed to post the scientific data "Put
your research data online today with Mendeley Data". The site reports, that Mendeley
Data is a secure cloud-based repository where you can store your data, providing it is
easy to exchange, access and cite, wherever you are [21]. The social network myExperiments, a repositore of workflows, is intended to share experimental data and research objects using software Taverna, RapidMinter, LONI Pipeline etc., helps scientists to plan
their own experiments based on the experience of predecessors [22].
So, scientific e-documents are being still evolved, but they retain the cultural and
scientific demands with regard to quality and integrity. They have a long way to go, and
it’s difficult to forecast what way their formats will change, but are becoming a modern
tool of specialists collaboration and science development.
References
[1] Mackenzie O. (Ed.) (2007) The scientific article in the age of digitization. — Dordrecht,
Springer.
[2] What are altmentrics? Altmetric. URL: https://www.altmetric.com/about-altmetrics/what-are-
altmetrics/
[3] Busygina T. V. (2011) Trudy GPNTB SO RAN, 2:289-295. [In Rus].
[4] Guides
to e-book formats. eBooks.com.
gb/articles/213875366-Guide-to-ebook-formats
URL:
https://support.ebooks.com/hc/en-
[5] Raggett D., Lam J., Alexander I. F., Kmiec M. (1998) Raggett on HTML 4. 2nd ed. Harlan,
Addison-Wesley. Doi: 10.1108/intr.1999.17209baf.005/full/html
[6] CAS REGISTRY and CAS Registry Number FAQs. CAS: a division of the American Chem-
ical Society. URL: https://www.cas.org/support/documentation/chemical-substances/faqs
[7] Is your chemical R&D data siloed? Reaxys. URL: https://www.elsevier.com/solutions/reaxys
[8] ISO 32000-1:2008 Document management — portable document format. International Or-
ganization for Standardization (2008) URL: https://www.iso.org/standard/51502.html
[9] PDF.
Three
letters
that
changed
the
world.
https://acrobat.adobe.com/us/en/acrobat/about-adobe-pdf.html
83
Adobe.
URL:
Busygina T. V.,
Rykova V. V.
Formats of scientific e-documents in the modern
information-communication space
[10] Bredikhin S. V., Kuznetsov A. Yu., Shcherbakova N. D. (2013) Analiz tsitirovaniya v biblio-
metrii (Novosibirsk, IVMiMG SO RAN, NEICON). [In Rus].
[11] Wolfram S. (2002) A new kind of science. S. l. (Wolfram Media).
[12] Computable document format. Wolfram: computation meet knowledge (2017) URL:
http://www.wolfram.com/cdf/?source=nav
[13] Modern
technical
computing.
https://www.wolfram.com/mathematica/
Wolfram
Mathematica
[14] CDF
licensing options. Wolfram: computation meet knowledge
http://www.wolfram.com/cdf/adoptingcdf/licensing-options.html
(2017)
(2017)
URL:
URL:
[15] Berners-Lee T., Hendler J., Lassila J. (2001) Scientific American, 284(5):35–43.
[16] Open data in a big data world. Science International (2016) URL: http://www.science-
international.org/
[17] Berners-Lee T. (2006) Design Issues. Linked Data. W3C. URL: https://www.w3.org/
DesignIssues/LinkedData.html
[18] Kircz J. G. (2001) New practices for electronic publishing. Learned Publishing. Pt. 1: Will
the scientific paper keep its form, 14(4):27–32. Doi: 10.1087/095315101753141365 ; Pt. 2:
New forms of the scientific paper. 2002, 15(1):27–32. Doi: 10.1087/095315102753303652.
[19] Main journal page. Videonauka: nauchnyi zhurnal. URL: https://videonauka.ru/ [In Rus]
[20] Bartling S., Friesike S. (eds.) (2014) Opening science: the evolving guide on how the internet
is changing research, collaboration and scholarly publishing (Heidelberg etc., Springer
Open).
[21] Discover Mendeley data. Mendeley. URL: https://data.mendeley.com/
[22] De Roure D., Goble C., Stevens R. (2009) Future Generation Computer Systems, 25(5):561–
567.
Форматы научных электронных документов в современном
информационно-коммуникационном пространстве
Т. В. Бусыгина, В. В. Рыкова
Государственная публичная научно-техническая библиотека Сибирского отделения Российской академии наук,
630102, Новосибирск, ул. Восход, 15
e-mail: busygina @spsl.nsc.ru, rykova @spsl.nsc.ru
Аннотация. В статье рассматривается проблема существования научного е-документа в электронной
среде. Цель исследования: дать краткую характеристику форматов научных документов (HTML, PDF,
CDF), показать их преимущества и недостатки. В работе описаны: 1) широко используемые форматы
HTML (HyperText Markup Language) и PDF (Portable Document Format); 2) охарактеризован формат
будущего — CDF (Computable Document Format); форматы, описания данных (в частности, научных)
по стандарту RDF (Resource Description Framework), содержащие открытые связанные данные (Linked
Open Data). Он использует преимущества традиционного существования научного документа в элек-
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тронной форме. К ним относятся: включение текстовых и нетекстовых элементов (3D-изображения,
звук); выполнение расчетов и внесение изменений непосредственно в файл документа; гиперссылки
на интернет-пространство или другие файлы, расположенные локально в компьютере; создание открытых связанных научных данных, обсуждение документа в электронном научном пространстве в
режиме реального времени. Электронный научный документ — современное средство научной коммуникации, инкорпорированное в развивающуюся цифровую научную инфраструктуру.
Ключевые слова: научный документ, формат электронного документа, HyperText Markup Language
(HTML), Portable Document Format (pdf), Computable Document Format (cdf).
Литература
[1] The scientific article in the age of digitization / Ed.: O. Mackenzie. — Dordrecht, Springer, 2007.
[2] What are altmentrics? Altmetric. [Электронный документ] URL: https://www.altmetric.com/aboutaltmetrics/what-are-altmetrics/
[3] Бусыгина T. В. Как прочитать электронную книгу? // Труды ГПНТБ СО РАН. 2011. № 2. С. 289–
295.
[4] Guides
to
e-book
formats.
eBooks.com
[Электронный
документ]
https://support.ebooks.com/hc/en-gb/articles/213875366-Guide-to-ebook-formats
URL:
[5] Raggett D., Lam J., Alexander I. F., Kmiec M. Raggett on HTML 4. 2nd ed. — Harlan, Addison-Wesley, 1998.
[6] CAS REGISTRY and CAS Registry Number FAQs. CAS: a division of the American Chemical Society.
[Электронный документ] URL: https://www.cas.org/support/documentation/chemical-substances/faqs
[7] Is
your
chemical
R&D
data
siloed?
Reaxys
[Электронный
https://www.elsevier.com/solutions/reaxys (дата обращения 11.07.2019)
документ]
URL:
[8] ISO 32000-1:2008 Document management — portable document format. International Organization for
Standardization. 2008 [Электронный документ] URL: https://www.iso.org/standard/51502.html
[9] PDF. Three letters that changed the world. Adobe.
https://acrobat.adobe.com/us/en/acrobat/about-adobe-pdf.html
[Электронный
документ]
URL:
[10] Бредихин С. В., Кузнецов А. Ю., Щербакова Н. Г. Анализ цитирования в библиометрии. — Новосибирск : ИВМиМГ СО РАН, НЭИКОН, 2013.
[11] Wolfram S. A new kind of science. [S. l.]. — Wolfram Media, 2002.
[12] Computable document format. Wolfram: computation meet knowledge. 2017 [Электронный документ]
URL: http://www.wolfram.com/cdf/?source=nav
[13] Modern technical computing. Wolfram Mathematica. 2017 [Электронный документ] URL:
https://www.wolfram.com/mathematica/
[14] CDF licensing options. Wolfram: computation meet knowledge. 2017 [Электронный документ] URL:
http://www.wolfram.com/cdf/adoptingcdf/licensing-options.html
[15] Berners-Lee T., Hendler J., Lassila J. The semantic web // Scientific American, 2001. Vol. 284. No. 5. P.
35–43.
[16] Open data in a big data world. Science International. 2016 [Электронный документ] URL:
http://www.science-international.org/
[17] Berners-Lee T. Design Issues. Linked Data. W3C. 2006 [Электронный документ] URL:
https://www.w3.org/DesignIssues/LinkedData.html
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information-communication space
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Авторы:
Татьяна Владимировна Бусыгина — кандидат биологических наук, ведущий научный сотрудник, заведующий отделом научной библиографии, Государственная публичная научно-техническая библиотека Сибирского отделения Российской академии наук
Валентина Викторовна Рыкова — старший научный сотрудник отдела научной библиографии, Государственная публичная научно-техническая библиотека Сибирского отделения Российской академии наук
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