JROST OSS research
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Open science tools: JROST ecosystem overview research (presentation: https://docs.google.com/presentation/d/1VlPToLvF71ZIWvqClO-A21d2u9grO9pQf17G_z76ge0/edit?usp=sharing)
August 2018 by Lettie Y. Conrad (@lyconrad)
Note: This table uses the Kramer / Bosman research-phase taxonomy (http://bit.ly/innoscholcomm-list) and many of the same tool classifications, applying stricter, hard-science focused criteria in the definition of 'open'
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Research phase
Information need / task
OS tool per phaseName of OS toolPurpose / valueProvider / URLDiscipline Specific / Agnostic
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Preparationproject management1Open Science Frameworksuite of research lifecycle tools / servicesCenter for Open ScienceDA
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crowdsource/define research priorities/ideas/collaborations3Journal of Brief Ideasindex of research ideas available for public scrutiny, voting, commentaryZenodo-powered crowdsourced journalDA
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VIVOindex of researchers, scholarship, institutions for discovery, collaborationDuraSpaceDA
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SciStartercitizen science registry, project recruiting, trackingArizona State UniversityDA
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fund / get contract3Thinklabscience news around topical communities, researchers for hireThinklabDA
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FundRefsearch index of research grant organizationsCrossrefDA
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SciFundtrain / encourage researchers in their outreach activities; connect public directly to scientists; crowdfundingSciFundDA
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Discoverysearch (lit/data/patents/code)23Crystallography Open DatabaseOA database of crystal structures of organic, inorganic, metal-organic compounds and mineralsCODDS
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CERN Open Dataopen datasets from particle physics researchCERNDS
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DataBankOA global development / economic dataWTODS
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OpenPHACTSsearch index of linked public data re: applied life science / pharmaOpen PHACTS FoundationDS
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PaleoBioDBpublic database of paleo research datasetPBDB (via NSF grants)DS
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Yale Image FinderPubMed Central (NIH OA database) search by image / figureYale (?)DA
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Paperitymultidisciplinary OA article aggregator, search, alerts, newsPaperity (n/p)DA
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OpenGreymultidisciplinary European grey literature (conference reports, dissertations, etc.)INIST-CNRSDA
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Open Knowledge Mapsvisual search of open science (searches either PubMed or BASE)Open Knowledge MapsDA
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OpenAIREplatform offering OA publication support, linking, and content searchOpenAIRE2020DA
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OAIstersearchable index of OA repositoriesOCLCDA
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BASE (Bielefeld Academic Search Engine)multidisciplinary metadata search engine, 60% OA contentBielefeld University LibraryDA
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COREsearchable index of OA journals, repositories, archivesCOREDA
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PrePubMedaggregated search across 5 popular preprint serversOmnes ResDA
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PubMed Centralfull-text repository of OA articles (medical)NCBI/NIHDS
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Crossref Metadata SearchDOI metadata search indexCrossrefDA
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OSF Preprint Searchaggregated search across 27 OSF and popular preprint serversOSFDA
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LA Referenciafederated network of institutional repositories in Latin AmericaLA ReferenceDA
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MetaAI search engine, recommendations, analysis for biomedical researchCZIDS
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Research and Education Space (RES) search platform for digital collections of UK libraries, museums, media, etc.Partnership of BBC, JISC, etc.DA
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Wikipediacommunity-driven online reference toolWikimedia FoundationDA
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Text Analyzerliterature search via text analysis of relevant articles, chapters, other textJSTORDA
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Open Citations Corpusopen citation and open data search, infrastructure, advocacy, open standardsComp Sci / Engineering Dept., University of BolognaDA
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get access4Unglue itenables free ebooks in partnership with authors, institutions, etc.Free Book FoundationDA
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Open Access Buttonsearch and retrieval of free, legal full-text articles, site + browser extensionOpen Access ButtonDA
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Hinarifree or low-cost access to scholarly content for local & non-profits in developing countriesWHODA
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Unpaywallharvests OA publication data for search, retrieval, trackingImpact storyDA
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get alerts / get (reading) recommendations0JournalTOCsCollects ToCs (Tables of Contents) from 31,755 journals and offers customizable alert servicesJournalTOCsDA
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get alerts / get (reading) recommendations0Observatory of International RelationsLists the latest papers from Political Science journalsOOIRDS
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get alerts / get (reading) recommendations0The Philosophy PaperboyLists the latest papers from Philosophy journalsThe Philosophy PaperboyDS
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reference management3RefBankcollaborative bibliography of biodiversity literatureRefBankDA
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CiteUlikereference sharing, managementCiteUlikeDA
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Zoteroreference & document management, organization, citation formatting, tagging, etc.MozillaDA
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read / view0
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annotate/tag (during/after reading)3PeerLibrarycollaborative discovery, annotations, collectionsPeerLibraryDA
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TagTeamtagging platform and feed aggregatorTagTeamDA
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PubPeerbrowser plug-in to support online journal clubs (reading, analysis, comments)PubPeerDA
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Experiment / analyzeexperiment & collect/mine/extract data10ManyLabs"fosters dialogue on emerging science-based technologies" (atmospheric carbon dioxide removal)ManyLabsDS
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Morph.ioautomated web scraping, formatted for coding / computationMorph.ioDA
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Eyewireonline game to contribute data for 3D map the human brain, citizen scienceEyewireDS
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Leukipposcloud-based bioengineering labThe Leukippos InstituteDS
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OpenML"open, organized, online ecosystem for machine learning" (data science / math)OpenMLDS
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BioToolsportal of bioinformatics resources and tools for discovery, interoperabilityElixir DenmarkDS
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Hackuariumcommunity and online biology lab ("biohacking")Univercite, Inartis FoundationDS
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OpenTrialslocate, match, share public data, docs on clinical trialsCenter for Open ScienceDS
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eagle-isharing, discovery, networking for biomed researcherseagle-i NetworkDS
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Biometrics Evaluation and Testing (BEAT)"computing e-infrastructure" for sharing biometric data, codeIdiap Research InstituteDS
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collaboration, sharing notebooks / protocols3Open Notebook Science Networkhosting OA research notebooks, powered by WordPressONSNetworkDA
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Synapsebio-science research collaboration platformSage BionetworksDS
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Jupyter Notebookscollaboration / publishing of notebooks produced with JupyterProject JupyterDA
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analyze11Keplerdesign, execute, share scientific and computational models, workflowsThe Kepler ProjectDA
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Galaxyonline data manipulation, analysis (biomedical)The Galaxy ProjectDS
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BOINCopen source volunteer & grid computing (computer, data science)University of CaliforniaDS
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Bioconductorstat analysis for R-based datasetsBioconductor ProjectDS
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Jupyterinteractive data science analysis, computer processing of scientific dataProject JupyterDS
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SciPycommunity-driven suite of tools (e.g., NumPy) for Python processing, plotting, analysisSciPyDA
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rOpenScisearch, access, share, interact with scientific data using R packagesrOpenSciDA
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Folding@homedistributed computing project for protein research (medical sciences)Pande LabDS
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Project Noahwildlife research, search, discovery, citizen science platform (biology, environmental sciences)Project NoahDS
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Zooniverse"people-powered research" platform, crowdsourced data, analysisZooniverseDA
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Open Data Fitopen source tools for computational experiments, data processing, analysisConvergent Bio-Nano Science & TechnologyDA
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Writingvisualize2WorldMapopen map creation, sharingHarvard CollegeDS
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Kepler.glgeospatial visualization tool for large datasetsVis.glDS
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write (+ code)1Scalaropen source, semantic web collaborative authoring, publishing platformAliance for Networking Visual CultureDA
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cite0
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translate0
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Dissemination & Publicationarchive/share code, data17Binderpilot cloud service for sharing code, notebooksThe Binder TeamDA
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RunMyCodeonline repository for sharing code, findings, datasetsRunMyCodeDA
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Exec&Shareweb service to share, run computer code, multidisciplinaryExec&ShareDA
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NeuroVaultpublic repository of neuroimaging data, statistical maps, etc. (neurology)NeuroVaultDS
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ASCLrepository of astrophysical source codeAstrophysics Source Code LibraryDS
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BioLINCCrepository of biologic specimen dataNational Heart, Lung, and Blood Institute (NIH)DS
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GBIF Datafree, open biodiversity datasetsGlobal Biodiversity Information FacilityDS
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ICSU-WDS Data Portal prototype data-sharing system for space, geosciencesWorld Data Systems, International Council for ScienceDS
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Knowledge Network for Biocomplexityinternational repository of ecological and environmental research data, findingsKNBDS
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DataONEnetwork of environmental science repositories for research, data sharing, discoveryData Observation Network for EarthDS
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openSNPsharing genetic test results, literature, research dataopenSNPDS
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GEO (Gene Expression Omnibus)public genomics repository for data sharingNCBI / NIHDS
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Dryad Digital Repositorycloud storage, sharing of datasets, linked to articlesDryadDA
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Datdata sharing protocol to share, archive scientific datasetsDat ProjectDA
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B2SHAREpublic research data repository for sharing, searchEUDATDA
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ZenodoOA repository for EU-funded research data, papersOpenAIREDA
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Dashnetwork of UC repositories for research, data sharing (e.g., DataONE)University of CaliforniaDA
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archive/share publications6Open Science Repositoryindependent project facilitating open review, publication of articles by disciplinary collectionunknownDA
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HALFrench multidisciplinary open archiveCCSDDA
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viXra"e-print archive of scientific work" aimed at capturing rejected ArXiv articlesviXraDS
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ArXivSTM-focused preprint platformCornell University LibraryDS
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bioRxivpreprint server for biologyCold Spring Harbor LaboratoryDS
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EngrXivpreprint server for engineering, ArXiv spin off, hosted with OSFUniversity of Wisconsin-StoutDS
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archive/share presentations/posters1ESSOArposter and preprint server for earth / space science researchESSOArDS
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present research findings1CEUR Workshop Proceedingscomputer science presentations, conference proceedingsCEUR-WSDS
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