{"id":16890989,"url":"https://github.com/alandefreitas/bibexplorer","last_synced_at":"2025-04-11T13:10:35.182Z","repository":{"id":139489805,"uuid":"296454747","full_name":"alandefreitas/bibexplorer","owner":"alandefreitas","description":"📚 BibExplorer: a tool to process curricula, extract article meta-data from various APIs, and calculate bibliometric indicators.","archived":false,"fork":false,"pushed_at":"2020-10-04T23:12:05.000Z","size":2199,"stargazers_count":7,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-05-21T04:02:42.371Z","etag":null,"topics":["bibliography","bibliometric-analysis","bibliometrics","indicator","science","science-research","scientific-computing","scientific-publications","scientific-visualization"],"latest_commit_sha":null,"homepage":"https://alandefreitas.github.io/bibexplorer/","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/alandefreitas.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"docs/contributing.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2020-09-17T22:22:30.000Z","updated_at":"2024-05-21T04:02:42.373Z","dependencies_parsed_at":null,"dependency_job_id":"75fd7395-2f7c-40e6-b9ae-7db82f58ed3c","html_url":"https://github.com/alandefreitas/bibexplorer","commit_stats":{"total_commits":45,"total_committers":5,"mean_commits":9.0,"dds":0.2666666666666667,"last_synced_commit":"8b81af72d93d3a947e1e1157204b318e51a68121"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alandefreitas%2Fbibexplorer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alandefreitas%2Fbibexplorer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alandefreitas%2Fbibexplorer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alandefreitas%2Fbibexplorer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alandefreitas","download_url":"https://codeload.github.com/alandefreitas/bibexplorer/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248405054,"owners_count":21097885,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bibliography","bibliometric-analysis","bibliometrics","indicator","science","science-research","scientific-computing","scientific-publications","scientific-visualization"],"created_at":"2024-10-13T17:05:14.371Z","updated_at":"2025-04-11T13:10:35.160Z","avatar_url":"https://github.com/alandefreitas.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BibExplorer 📚\n\n\u003e Process curricula, extract article meta-data, and calculate bibliometric indicators\n\n[![BibExplorer](docs/images/indicators_window.png)](https://alandefreitas.github.io/bibexplorer/)\n\n\u003cbr/\u003e\n\nBibliographic 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.\n\n\u003cbr/\u003e\n\n[![Build Status](https://img.shields.io/github/workflow/status/alandefreitas/bibexplorer/Build%20BibExplorer?event=push\u0026label=Build\u0026logo=Github-Actions)](https://github.com/alandefreitas/bibexplorer/actions?query=workflow%3A%22Build+BibExplorer%22+event%3Apush)\n[![Latest Release](https://img.shields.io/github/release/alandefreitas/bibexplorer.svg?label=Download)](https://GitHub.com/alandefreitas/bibexplorer/releases/)\n[![Docs](https://img.shields.io/website-up-down-green-red/http/alandefreitas.github.io/bibexplorer.svg?label=Documentation)](https://alandefreitas.github.io/bibexplorer/)\n\n\u003cbr/\u003e\n\n\u003c!-- 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START doctoc generated TOC please keep comment here to allow auto update --\u003e\n\u003c!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE --\u003e\n\u003cdetails\u003e\n\u003csummary\u003eTable of Contents\u003c/summary\u003e\n\n- [Examples](#examples)\n  - [Input formats](#input-formats)\n  - [Running BibExplorer](#running-bibexplorer)\n  - [Indicators](#indicators)\n  - [Timeline](#timeline)\n  - [Stability](#stability)\n  - [Compare](#compare)\n  - [Correlations](#correlations)\n  - [Citations](#citations)\n- [Install](#install)\n  - [Packages](#packages)\n  - [Build from source](#build-from-source)\n- [Limitations](#limitations)\n- [Contributing](#contributing)\n  - [Contributors](#contributors)\n- [References](#references)\n\n\u003c/details\u003e\n\u003c!-- END doctoc generated TOC please keep comment here to allow auto update --\u003e\n\n## Examples\n\n### Input formats\n\nCreate a directory for the CVs and save them in one of the following formats.\n\n#### CSV\n\nA CSV file should have the following columns:\n\n* Author ID\n* Author\n* Paper ID\n* Title\n* Journal\n* Year\n* Authors\n* Citations\n\nSee an example in [`resources/examples/input/ringo.csv`](resources/examples/input/ringo.csv). \n\nEven 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.\n\nThe \"Authors\" should be separated by commas so that BibExplorer can properly identify the number of authors in each paper.\n\n#### JSON\n\nA JSON file should have the following fields:\n\n* Author ID\n* Author\n* Papers\n\nSee an example in [`resources/examples/input/satoshi.json`](resources/examples/input/satoshi.json). \n\nThe \"Author ID\" field might have a number or a string. And \"Papers\" is a list of papers where each paper has the following fields:\n\n* Paper ID\n* Title\n* Journal\n* Year\n* Authors\n* Citations\n\nThe \"Paper ID\" can also be a string or a number. The \"Authors\" field should be a list of strings.\n\n#### Lattes XML\n\nXML files are parsed as CVs from the [lattes platform](http://buscatextual.cnpq.br/buscatextual/busca.do). To download a CV in XML  format from the platform, open a CV, and use the menu on the top right.\n\n![](docs/images/lattes_xml.png)\n\nOr simply use the URL:\n\n```\nhttp://buscatextual.cnpq.br/buscatextual/download.do?metodo=apresentar\u0026idcnpq=\u003clattes_id\u003e\n```\n\n### Running BibExplorer\n\nUse 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:\n\n```bash\nbibexplore --input ./input \n```\n\nor simply\n\n```bash\nbibexplore --i ./input \n```\n\nYou 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.\n\nBibExplorer will start processing all CVs. You can keep track of its progress with the \"Processing\" window:\n\n![](docs/images/processing_window.png)\n\nFor each paper, it will use the available APIs to look for information such as the number of citations the paper has.\n\nAs BibExplorer processes more papers, the indicators instantly become available in the \"Indicators\" window.\n\n![](docs/images/indicators_window.png)\n\n### Indicators\n\nThe 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:\n\n![](docs/images/summary_tab.png)\n\nThe indicator window can show each indicator from numerous perspectives.\n\n### Timeline\n\nThe \"Timeline\" tab shows how indicators have changed over time for each researcher.\n\n![](docs/images/indicators_window.png)\n\nYou can adjust the \"Time Window\" parameter to choose how many years are considered in an indicator. \n\n![](docs/images/timeline_tab.png)\n\nThe 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.\n\nThe \"Table\" tab shows the same information in a heat table, which is better for comparisons rather than absolute values.\n\n![](docs/images/table_tab.png)\n\nResearchers are sorted by their indicators in the last year.\n\n### Stability\n\nThe \"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. \n\n![](docs/images/stability_tab.png)\n\nIn 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.\n\nFor 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. \n\nIf 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.\n\n### Compare\n\nThe \"Compare\" tab shows us how the researchers have performed in the last years under all indicators.\n\n![](docs/images/compare_tab.png)\n\nThe 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.\n\n### Correlations\n\nThe \"Correlations\" tab shows us the similarity of results we get from the various indicators.\n\n![](docs/images/correlations_tab.png)\n\nIf we only want to know whether the indicators would give us different rankings for the researchers, we can choose a non-parametric correlation.\n\n![](docs/images/correlations_non_parametric.png)\n\nThe last row tells us how good an indicator is at predicting all other indicators at once.\n\n### Citations\n\nThe \"Citations\" tab shows the distribution of the number of citations considering all authors at once.\n\n![](docs/images/citations_tab.png)\n\nThe 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. \n \n## Install\n\n### Packages\n\nGet the binary package from the [release section](https://github.com/alandefreitas/bibexplorer/releases). These binaries refer to the last release version of BibExplorer. \n\nIf you need a more recent version, you can download the [binary packages from the CI artifacts](https://github.com/alandefreitas/bibexplorer/actions?query=workflow%3A%22Build+BibExplorer%22+event%3Apush) or build the library [from the source files](#build-from-source).\n\nFor convenience, you might want to add the BibExplorer directory to \"`PATH`\": \n\n* [Windows](https://docs.alfresco.com/4.2/tasks/fot-addpath.html)\n* [Linux](https://linuxize.com/post/how-to-add-directory-to-path-in-linux/)\n* [Mac OS](https://www.architectryan.com/2012/10/02/add-to-the-path-on-mac-os-x-mountain-lion/)\n\n### Build from source\n\n#### Dependencies\n\nThis section lists the dependencies you need before installing BibExplorer from source:\n\n* C++17\n* CMake 3.14 or higher\n* OpenGL\n* Curl\n\n\u003cdetails\u003e\n    \u003csummary\u003eInstructions: Linux/Ubuntu/GCC\u003c/summary\u003e\n    \nCheck your GCC version\n\n```bash\ng++ --version\n```\n\nThe output should be something like\n\n```console\ng++-8 (Ubuntu 8.4.0-1ubuntu1~18.04) 8.4.0\n```\n\nIf you see a version before GCC-8, update it with\n\n```bash\nsudo apt update\nsudo apt install gcc-8\nsudo apt install g++-8\n```\n\nTo update to any other version, like GCC-9 or GCC-10:\n\n```bash\nsudo apt install build-essential\nsudo add-apt-repository ppa:ubuntu-toolchain-r/test\nsudo apt-get update\nsudo apt install g++-10\n```\n\nOnce 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:\n\n```bash\nsudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-7 7\nsudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-7 7\nsudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-10 10\nsudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 10\n```\n\nYou can now use `update-alternatives` to set you default `gcc` and `g++`:\n\n```bash\nupdate-alternatives --config g++\nupdate-alternatives --config gcc\n```\n\nCheck your CMake version:\n\n```bash\ncmake --version\n```\n\nIf it's older than CMake 3.14, update it with\n\n```bash\nsudo apt upgrade cmake\n```\n\nor download the most recent version from [cmake.org](https://cmake.org/).\n\n[Later](#build-the-examples) when running CMake, make sure you are using GCC-8 or higher by appending the following options:\n\n```bash\n-DCMAKE_C_COMPILER=/usr/bin/gcc-8 -DCMAKE_CXX_COMPILER=/usr/bin/g++-8\n```\n\nInstall OpenGL / GLFW3:\n\n```bash\nsudo apt-get install libglfw3-dev\n```\n\nInstall curl:\n\n```bash\nsudo apt install curl\nsudo apt-get install libcurl4-gnutls-dev\n```\n\nInstall OpenSSL:\n\n```bash\nsudo apt-get install libssl-dev\n```\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n    \u003csummary\u003eInstructions: Mac Os/Clang\u003c/summary\u003e\n\nCheck your Clang version:\n\n```bash\nclang --version\n```\n\nThe output should be something like\n\n```console\nApple clang version 11.0.0 (clang-1100.0.33.8)\n```\n\nIf you see a version before Clang 11, update XCode in the App Store or update clang with homebrew. \n\nCheck your CMake version:\n\n```bash\ncmake --version\n```\n\nIf it's older than CMake 3.14, update it with\n\n```bash\nsudo brew upgrade cmake\n```\n\nor download the most recent version from [cmake.org](https://cmake.org/).\n\nIf the last command fails because you don't have [Homebrew](https://brew.sh) on your computer, you can install it with\n\n```bash\n/bin/bash -c \"$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)\"\n```\n\nor you can follow the instructions in [https://brew.sh](https://brew.sh).\n\nDownload GLFW3 from https://www.glfw.org\n\nInstall OpenSSL:\n\n```bash\nbrew install openssl\n```\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n    \u003csummary\u003eInstructions: Windows/MSVC\u003c/summary\u003e\n    \n* Make sure you have a recent version of [Visual Studio](https://visualstudio.microsoft.com)\n* Install [Git](https://git-scm.com/download/win)\n* Install [CMake](https://cmake.org/download/)\n* Install [GLFW3](https://www.glfw.org)\n\nInstall [VCPKG](https://github.com/microsoft/vcpkg):\n\n```bash\ngit clone https://github.com/microsoft/vcpkg\n\u003e .\\vcpkg\\bootstrap-vcpkg.bat\n```\n\nInstall [libcurl](https://curl.haxx.se/download.html):\n\n```bash\nvcpkg install curl\n```\n\n\u003c/details\u003e\n\nSome 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](source/CMakeLists.txt).\n\n#### Build Only\n\nThis will build everything in `./build` directory:\n\n```bash\nmkdir build\ncmake -version\ncmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS=\"-O2\"\ncmake --build . -j 2 --config Release\n```\n\nOn windows, replace `-O2` with `/O2`. You can replace `2` in `-j 2` with the number of cores in your computer.\n\n#### Install from Source\n\nThis will install BibExplorer on your system:\n\n```bash\nmkdir build\ncmake -version\ncmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS=\"-O2\" \ncmake --build . -j 2 --config Release\ncmake --install .\n```\n\nOn windows, replace `-O2` with `/O2`. You might need `sudo` for this last command.\n\n#### Building the packages\n\nThis will create the binary packages you can use to install BibExplorer on your system:\n\n```bash\nmkdir build\ncmake -version\ncmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_FLAGS=\"-O2\"\ncmake --build . -j 2 --config Release\ncmake --install .\ncpack .\n```\n\nOn windows, replace `-O2` with `/O2`. You might need `sudo` for this last command.\n\n## Limitations\n\nWe have not integrated many APIs yet. [`docs/APIs.md`](docs/APIs.md) includes a list of APIs we are considering with their pros and cons. \n\nThe 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. \n\nWe 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.\n\n## Contributing\n\nThere are many ways in which you can contribute to this library:\n\n* Testing the library in new environments \u003csup\u003esee [1](https://github.com/alandefreitas/bibexplorer/issues?q=is%3Aopen+is%3Aissue+label%3A%22cross-platform+issue+-+windows%22), [2](https://github.com/alandefreitas/bibexplorer/issues?q=is%3Aopen+is%3Aissue+label%3A%22cross-platform+issue+-+linux%22), [3](https://github.com/alandefreitas/bibexplorer/issues?q=is%3Aopen+is%3Aissue+label%3A%22cross-platform+issue+-+macos%22) \u003c/sup\u003e\n* Including new indicators \u003csup\u003esee [1](#indicators)\u003c/sup\u003e\n* Integrating new APIs \u003csup\u003esee [1](#limitations)\u003c/sup\u003e\n* Improving this documentation \u003csup\u003esee [1](https://github.com/alandefreitas/bibexplorer/issues?q=is%3Aopen+is%3Aissue+label%3A%22enhancement+-+documentation%22) \u003c/sup\u003e\n* Finding bugs in general \u003csup\u003esee [1](https://github.com/alandefreitas/bibexplorer/issues?q=is%3Aopen+is%3Aissue+label%3A%22bug+-+compilation+error%22), [2](https://github.com/alandefreitas/bibexplorer/issues?q=is%3Aopen+is%3Aissue+label%3A%22bug+-+compilation+warning%22), [3](https://github.com/alandefreitas/bibexplorer/issues?q=is%3Aopen+is%3Aissue+label%3A%22bug+-+runtime+error%22), [4](https://github.com/alandefreitas/bibexplorer/issues?q=is%3Aopen+is%3Aissue+label%3A%22bug+-+runtime+warning%22)\u003c/sup\u003e\n* Whatever idea seems interesting to you\n\nIf 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.\n\n\u003cdetails\u003e\n    \u003csummary\u003eExample: CLion\u003c/summary\u003e\n    \n![CLion Settings with Pedantic Mode](docs/images/pedantic_clion.png)\n    \n\u003c/details\u003e\n\n### Contributors\n\n\u003c!-- readme: collaborators,contributors -start --\u003e \n\u003ctable\u003e\n\u003ctr\u003e\n    \u003ctd align=\"center\"\u003e\n        \u003ca href=\"https://github.com/alandefreitas\"\u003e\n            \u003cimg src=\"https://avatars0.githubusercontent.com/u/5369819?v=4\" width=\"100;\" alt=\"alandefreitas\"/\u003e\n            \u003cbr /\u003e\n            \u003csub\u003e\u003cb\u003eAlan De Freitas\u003c/b\u003e\u003c/sub\u003e\n        \u003c/a\u003e\n    \u003c/td\u003e\n    \u003ctd align=\"center\"\u003e\n        \u003ca href=\"https://github.com/hodfernando\"\u003e\n            \u003cimg src=\"https://avatars1.githubusercontent.com/u/30090567?v=4\" width=\"100;\" alt=\"hodfernando\"/\u003e\n            \u003cbr /\u003e\n            \u003csub\u003e\u003cb\u003eFernando Henrique Oliveira Duarte\u003c/b\u003e\u003c/sub\u003e\n        \u003c/a\u003e\n    \u003c/td\u003e\u003c/tr\u003e\n\u003c/table\u003e\n\u003c!-- readme: collaborators,contributors -end --\u003e\n\n## References\n\nThese are some references we used for this work:\n\n1)  G. Abramo, T. Cicero, and C. A. DbAngelo. Assessing the varying level of impact measurement accuracy as a function of the citation window length. Journal of Informetrics, 5(4):659b 667, 2011.\n\n2)  D. E. Acuna, S. Allesina, and K. P. Kording. Future impact: Predicting scientific success. Nature, 489(7415):201, 2012.\n\n3)  A. A. Agrawal. Corruption of journal impact factors. TRENDS in Ecology and Evolution, 20(4):157, 2005.\n\n4)  S. Alonso, F. Cabrerizo, E. Herrera-Viedma, and F. Herrera. hg-index: A new index to characterize the scientific output of researchers based on the h-and g-indices. Scientometrics, 82(2):391b 400, 2009.\n\n5)  S. Alonso, F. J. Cabrerizo, E. Herrera-Viedma, and F. Herrera. h-index: A review focused in its variants, computation and standardization for different scientific fields. Journal of informetrics, 3(4):273b 289, 2009.\n\n6)  V. Anauati, S. Galiani, and R. H. GC!lvez. Quantifying the life cycle of scholarly articles across fields of economic research. 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