{"id":19327984,"url":"https://github.com/inab/biolitmap","last_synced_at":"2025-04-22T21:30:38.150Z","repository":{"id":70375639,"uuid":"123899968","full_name":"inab/BIOLITMAP","owner":"inab","description":"Code for the paper \"BIOLITMAP: a web-based geolocated and temporal visualization of the evolution of bioinformatics publications\" in Oxford Bioinformatics.","archived":false,"fork":false,"pushed_at":"2019-05-03T15:37:53.000Z","size":2628,"stargazers_count":20,"open_issues_count":0,"forks_count":3,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-04-02T04:04:11.219Z","etag":null,"topics":["data-mining","data-science","data-visualization","machine-learning","maps","natural-language-processing","research","research-paper","science","social-analytics-team"],"latest_commit_sha":null,"homepage":"http://socialanalytics.bsc.es/biolitmap/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-2.1","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/inab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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":"2018-03-05T09:59:42.000Z","updated_at":"2022-05-15T16:19:40.000Z","dependencies_parsed_at":"2023-02-24T16:00:19.082Z","dependency_job_id":null,"html_url":"https://github.com/inab/BIOLITMAP","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inab%2FBIOLITMAP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inab%2FBIOLITMAP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inab%2FBIOLITMAP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/inab%2FBIOLITMAP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/inab","download_url":"https://codeload.github.com/inab/BIOLITMAP/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250328109,"owners_count":21412562,"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":["data-mining","data-science","data-visualization","machine-learning","maps","natural-language-processing","research","research-paper","science","social-analytics-team"],"created_at":"2024-11-10T02:19:40.397Z","updated_at":"2025-04-22T21:30:36.256Z","avatar_url":"https://github.com/inab.png","language":"Python","readme":"# BIOLITMAP: a web-based geolocated and temporal visualization of the evolution of bioinformatics publications\n\n## Description\n\nCode for the web-based geolocated and temporal visualization of bioinformatics research (BIOLITMAP): http://socialanalytics.bsc.es/biolitmap/.\n\nPaper accepted to Oxford Bioinformatics.\n\n## Directory structure\n\n* In /data the export of the BIOLITMAP SQL database is stored, as it was in December 2017.\n* In /scripts the tools used for the NLP tasks are stored\n* /scripts/src stores the codes related to the NLP, Clustering, Topic Modeling and Perplexity Analysis tasks.\n* /scripts/vis stores the visualization created using the final Latent Dirichlet Allocation model, by employing the pyLDAvis package.\n* /API stores the source codes of the REST API.\n\n## Getting the data from the REST API\n\nWe have deployed in our servers a REST API to gather the data from the map in JSON format, the following endpoints are available:\n\n1) http://socialanalytics.bsc.es/biolitmap-api/biolitmap/list - To get the complete list of the data.\n2) http://socialanalytics.bsc.es/biolitmap-api/biolitmap/filter/source/\"journal\" - To filter by source (e.g. Oxford Bioinformatics).\n3) http://socialanalytics.bsc.es/biolitmap-api/biolitmap/filter/year/[+-]\"year\" - To filter by year (e.g. 2010), you can use the + and - symbols to query for greater-equal or less-equal, respectively (e.g. +2010 or -2010).\n4) http://socialanalytics.bsc.es/biolitmap-api/biolitmap/filter/nameAffiliation/\"institution\" - To filter by research institution (e.g. University of Cambridge).\n  \n### Example output from the /list endpoint\n\n\u003cdiv style=\"text-align:center\"\u003e\u003cimg src=\"https://i.imgur.com/rC8VHO9.png\" /\u003e\u003c/div\u003e\n\n\n## Getting the raw source data from Scopus\n\nIn order to obtain the raw source data with which this application has been built on, the following steps need to be followed:\n\n1) Access to the Scopus (www.scopus.com) document search tool\n2) Search the documents by using the following query: \n\n``ISSN ( 'JOURNAL_ISSN' ) AND ( LIMIT-TO ( PUBYEAR , 2017 ) OR LIMIT-TO ( PUBYEAR , 2016 ) OR LIMIT-TO ( PUBYEAR , 2015 ) OR LIMIT-TO ( PUBYEAR , 2014 ) OR LIMIT-TO ( PUBYEAR , 2013 ) OR LIMIT-TO ( PUBYEAR , 2012 ) OR LIMIT-TO ( PUBYEAR , 2011 ) OR LIMIT-TO ( PUBYEAR , 2010 ) OR LIMIT-TO ( PUBYEAR , 2009 ) OR LIMIT-TO ( PUBYEAR , 2008 ) OR LIMIT-TO ( PUBYEAR , 2007 ) OR LIMIT-TO ( PUBYEAR , 2006 ) OR LIMIT-TO ( PUBYEAR , 2005 ) ) AND ( LIMIT-TO ( EXACTKEYWORD , \"Article\" ) )``\n\n3) Export the documents in CSV format with the 'Export' option.\n\n## Journals\n\nIn this first version of the application, the articles from the following journals are extracted:\n\n1) Oxford Bioinformatics (ISSN 1460-2059)\n2) Nucleic Acids Research (ISSN 1362-4962)\n3) BMC Bioinformatics (ISSN 1471-2105)\n4) BMC Genomics (ISSN 1471-2164)\n5) PLoS Computational Biology (ISSN 1553-734X)\n\n## Contact\n\nYou can contact the developers by sending an email to adrian.bazaga@bsc.es or maria.rementeria@bsc.es\n\n## Preview\n\n\u003cdiv style=\"text-align:center\"\u003e\u003cimg src=\"https://i.imgur.com/iIvs1P8.png\" /\u003e\u003c/div\u003e\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finab%2Fbiolitmap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finab%2Fbiolitmap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finab%2Fbiolitmap/lists"}