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BibExplorer 📚

Process curricula, extract article meta-data, and calculate bibliometric indicators

BibExplorer


Bibliographic indicators are a crucial complement to peer reviews. The careless use of indicators reduces the motivation for high-impact publications, creates incentives for unethical practices, leads to injustices, wastes money, and consumes the time of the community. Still, adequate evaluation methods demand elaborate algorithms and treating large volumes of data from multiple data sources. BibExplorer is a tool to process curriculums, extract article meta-data from various APIs, and calculate indicators. BibExplorer can reveal how the various indicators have fluctuated over time with custom time windows, estimate which indicators adequately predict future productivity, contrast the outcomes of indicators, measure their correlation, and provide numerous visualization tools to explore this information.


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Table of Contents

Examples

Input formats

Create a directory for the CVs and save them in one of the following formats.

CSV

A CSV file should have the following columns:

  • Author ID
  • Author
  • Paper ID
  • Title
  • Journal
  • Year
  • Authors
  • Citations

See an example in resources/examples/input/ringo.csv.

Even though there are columns for "Author ID" and "Author", a CSV file used as input should have information for a single author. This redundant information is used to make it compatible with the CSV files later generated to the output directory.

The "Authors" should be separated by commas so that BibExplorer can properly identify the number of authors in each paper.

JSON

A JSON file should have the following fields:

  • Author ID
  • Author
  • Papers

See an example in resources/examples/input/satoshi.json.

The "Author ID" field might have a number or a string. And "Papers" is a list of papers where each paper has the following fields:

  • Paper ID
  • Title
  • Journal
  • Year
  • Authors
  • Citations

The "Paper ID" can also be a string or a number. The "Authors" field should be a list of strings.

Lattes XML

XML files are parsed as CVs from the lattes platform. To download a CV in XML format from the platform, open a CV, and use the menu on the top right.

Or simply use the URL:

http://buscatextual.cnpq.br/buscatextual/download.do?metodo=apresentar&idcnpq=<lattes_id>

Running BibExplorer

Use the "--input" (or "-i") option to define the input directory with CVs. For instance, if you keep the CVs in a directory ./input, run BibExplorer with:

bibexplore --input ./input

or simply

bibexplore --i ./input

You can also use the --output (or -o) option to choose a directory for the results. Use the option --help (or -h) to see all other options. Any option not provided in the command line will be replaced by an option in a config.json file.

BibExplorer will start processing all CVs. You can keep track of its progress with the "Processing" window:

For each paper, it will use the available APIs to look for information such as the number of citations the paper has.

As BibExplorer processes more papers, the indicators instantly become available in the "Indicators" window.

Indicators

The bibliometric indicators are defined by (i) the weight we attribute to a paper, (ii) the constraints to even consider a paper, and (iii) the normalization strategy. The "Summary" tab includes a brief explanation for each indicator:

The indicator window can show each indicator from numerous perspectives.

Timeline

The "Timeline" tab shows how indicators have changed over time for each researcher.

You can adjust the "Time Window" parameter to choose how many years are considered in an indicator.

The wider the time window, the more stable the indicators should be. A maximum time window would show how much a researcher has produced up to that year.

The "Table" tab shows the same information in a heat table, which is better for comparisons rather than absolute values.

Researchers are sorted by their indicators in the last year.

Stability

The "Stability" tab uses historical data to show how each indicator and each possible time window would perform if we used them to predict productivity according to the chosen combination of indicator and time window.

In the example above, we have chosen the H-Index with a time window of 7 years. Using historical data, the table shows us how each combination of indicator and time window for the last years would fare to predict the H-Index of a researcher in the next 7 years.

For instance, the row "Impact Factor" and the column "06" gives us 45%. That means the Impact Factor of a researcher in the last 6 years has a non-parametric correlation of 45% with the H-Index of this author in the following 7 years.

If we look at the rows, we see that "Papers" is a very bad predictor of a researcher "H-Index" in the next 7 years. If we look at the columns, we see that, for our database, longer time windows have always tended to always give us a better prediction of the researcher's H-Index in the next 7 years.

Compare

The "Compare" tab shows us how the researchers have performed in the last years under all indicators.

The chosen indicator is used to sort results by that indicator. This helps us see if the results with the chosen indicator are much different from the results we would get from other indicators.

Correlations

The "Correlations" tab shows us the similarity of results we get from the various indicators.

If we only want to know whether the indicators would give us different rankings for the researchers, we can choose a non-parametric correlation.

The last row tells us how good an indicator is at predicting all other indicators at once.

Citations

The "Citations" tab shows the distribution of the number of citations considering all authors at once.

The histogram also shows the H-Core for this group of researchers. The H-Core is the number h of papers with at least h citations.

Install

Packages

Get the binary package from the release section. These binaries refer to the last release version of BibExplorer.

If you need a more recent version, you can download the binary packages from the CI artifacts or build the library from the source files.

For convenience, you might want to add the BibExplorer directory to "PATH":

Build from source

Dependencies

This section lists the dependencies you need before installing BibExplorer from source:

  • C++17
  • CMake 3.14 or higher
  • OpenGL
  • Curl
Instructions: Linux/Ubuntu/GCC

Check your GCC version

g++ --version

The output should be something like

g++-8 (Ubuntu 8.4.0-1ubuntu1~18.04) 8.4.0

If you see a version before GCC-8, update it with

sudo apt update
sudo apt install gcc-8
sudo apt install g++-8

To update to any other version, like GCC-9 or GCC-10:

sudo apt install build-essential
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt install g++-10

Once you installed a newer version of GCC, you can link it to update-alternatives. For instance, if you have GCC-7 and GCC-10, you can link them with:

sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 7
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-7 7
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-10 10
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 10

You can now use update-alternatives to set you default gcc and g++:

update-alternatives --config g++
update-alternatives --config gcc

Check your CMake version:

cmake --version

If it's older than CMake 3.14, update it with

sudo apt upgrade cmake

or download the most recent version from cmake.org.

Later when running CMake, make sure you are using GCC-8 or higher by appending the following options:

-DCMAKE_C_COMPILER=/usr/bin/gcc-8 -DCMAKE_CXX_COMPILER=/usr/bin/g++-8

Install OpenGL / GLFW3:

sudo apt-get install libglfw3-dev

Install curl:

sudo apt install curl
sudo apt-get install libcurl4-gnutls-dev

Install OpenSSL:

sudo apt-get install libssl-dev
Instructions: Mac Os/Clang

Check your Clang version:

clang --version

The output should be something like

Apple clang version 11.0.0 (clang-1100.0.33.8)

If you see a version before Clang 11, update XCode in the App Store or update clang with homebrew.

Check your CMake version:

cmake --version

If it's older than CMake 3.14, update it with

sudo brew upgrade cmake

or download the most recent version from cmake.org.

If the last command fails because you don't have Homebrew on your computer, you can install it with

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

or you can follow the instructions in https://brew.sh.

Download GLFW3 from https://www.glfw.org

Install OpenSSL:

brew install openssl
Instructions: Windows/MSVC

Install VCPKG:

git clone https://github.com/microsoft/vcpkg
> .\vcpkg\bootstrap-vcpkg.bat

Install libcurl:

vcpkg install curl

Some other small dependencies, like header-only libraries, if not found, will be download at compile-time by the build script. You can see these dependencies in source/CMakeLists.txt.

Build Only

This will build everything in ./build directory:

mkdir build
cmake -version
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-O2"
cmake --build . -j 2 --config Release

On windows, replace -O2 with /O2. You can replace 2 in -j 2 with the number of cores in your computer.

Install from Source

This will install BibExplorer on your system:

mkdir build
cmake -version
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-O2" 
cmake --build . -j 2 --config Release
cmake --install .

On windows, replace -O2 with /O2. You might need sudo for this last command.

Building the packages

This will create the binary packages you can use to install BibExplorer on your system:

mkdir build
cmake -version
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS="-O2"
cmake --build . -j 2 --config Release
cmake --install .
cpack .

On windows, replace -O2 with /O2. You might need sudo for this last command.

Limitations

We have not integrated many APIs yet. docs/APIs.md includes a list of APIs we are considering with their pros and cons.

The CSV and JSON input formats have a "Citations" field where one can directly enter the number of citations for each paper. This can be used to mitigate this lack of APIs.

We currently use the Microsoft Academic API but it seems to be very limited to find data about most papers. We are still studying which APIs could provide us with more useful data.

Contributing

There are many ways in which you can contribute to this library:

  • Testing the library in new environments see 1, 2, 3
  • Including new indicators see 1
  • Integrating new APIs see 1
  • Improving this documentation see 1
  • Finding bugs in general see 1, 2, 3, 4
  • Whatever idea seems interesting to you

If contributing with code, please leave the pedantic mode ON (-DBUILD_WITH_PEDANTIC_WARNINGS=ON). This helps us ensure the software works with other compilers and operating systems.

Example: CLion

CLion Settings with Pedantic Mode

Contributors

alandefreitas
Alan De Freitas 		hodfernando
Fernando Henrique Oliveira Duarte

References

These are some references we used for this work:

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About

📚 BibExplorer: a tool to process curricula, extract article meta-data from various APIs, and calculate bibliometric indicators.

alandefreitas.github.io/bibexplorer/

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science bibliography scientific-visualization scientific-computing indicator scientific-publications science-research bibliometrics bibliometric-analysis

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BibExplorer Latest
Sep 17, 2020

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