Innovations & Tools

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In the end, we came up with the first of its kind publishing platform to combine Authoring, Reviewing, Publishing, Hosting and Archiving all in one place. Bearing the name <a href="http://arphahub.com/" target="_blank">ARPHA</a>, it is implemented to all Pensoft journals and offers a <a href="http://arphahub.com/about/services" target="_blank">wide range of services</a> also to other journals and publishers. ARPHA represents the first ever end-to-end, entirely XML-based commodity in the journal publishing industry.</p> </div> </div> <div class="accordion-border"> <div class="row middle-xs accordion-toggle"> <div class="col-xs start-xs">Pensoft Markup Tool (PMT)</div> <div class="col-xs-2 end-xs"><span class="plusminus">+</span></div> </div> <div class="accordion-content">Another quite tiresome and painstaking task an author needs to complete, while submitting a manuscript, is a sweeping amount of importing, referencing, cross-linking, interlinking, mapping, and so on. Implementing our extensive experience in semantic technology and innovations, Pensoft has developed the Pensoft Markup Tool (PMT).</div> </div> <div class="accordion-border"> <div class="row middle-xs accordion-toggle"> <div class="col-xs start-xs">Pensoft Wiki Converter (PWC)</div> <div class="col-xs-2 end-xs"><span class="plusminus">+</span></div> </div> <div class="accordion-content"> <p>While the Wiki environment is a fine example of a huge open access online space with immense potential in science, we have always known that we need to make use of it, in order to provide a best-quality experience to our users. This is how we came up with the Pensoft Wiki Converter (PWC), which turns the XML versions of our papers into Media-Wiki-based pages, such as <a href="http://species-id.net/" target="_blank">Species-ID.net</a>.</p> </div> </div> <div class="accordion-border"> <div class="row middle-xs accordion-toggle"> <div class="col-xs start-xs">OpenBiodiv</div> <div class="col-xs-2 end-xs"><span class="plusminus">+</span></div> </div> <div class="accordion-content" style="display: none;"> <p><a href="http://openbiodiv.net/" target="_blank">OpenBiodiv</a> is an Open Biodiversity Knowledgement Management System (OBKMS), comprising a knowledge graph, a Linked Open Dataset, an ontology (<a href="https://github.com/pensoft/openbiodiv-o/blob/master/openbiodiv-ontology.Rmd" target="_blank">OpenBiodiv-O</a>) and а website (<a href="http://openbiodiv.net/" target="_blank">http://openbiodiv.net/</a>). OpenBiodiv gathers biodiversity knowledge extracted from semantically enhanced biodiversity articles published by Pensoft and taxonomic treatments harvested by <a href="http://plazi.org/" target="_blank">Plazi</a> and exposes the links between and within articles and their content. The knowledge graph contains semantic statements about authors, articles, treatments, taxonomic names, examined materials, institutions, genomic sequences, habitats, localities, and more. It has a SPARQL endpoint (<a href="http://graph.openbiodiv.net/" target="_blank">http://graph.openbiodiv.net/</a>) where experienced users can write complex queries. The website is currently available in beta version and is continuously developed to enable a better user experience and to help accomplish the aim of OpenBiodiv: to make biodiversity knowledge easily findable and accessible both by humans and machines.</p> <p><iframe allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/HbFIIAXrVng" title="YouTube video player" width="100%"></iframe></p> </div> </div> <div class="accordion-border"> <div class="row middle-xs accordion-toggle"> <div class="col-xs start-xs">Nanopublications for Biodiversity</div> <div class="col-xs-2 end-xs"><span class="plusminus">+</span></div> </div> <div class="accordion-content" style="display: none;"> <p>Nanopublications allow researchers to ‘fragment’ their most important scientific findings into ‘pixels of knowledge’. They are the smallest units of publishable information: a scientifically meaningful assertion about anything that can be uniquely identified and attributed to its author and serve to communicate a single statement, its original source (provenance) and citation record (publication info). Nanopublications are fully expressed in a way that is both human-readable and machine-interpretable. The Nanopublications-for-Biodiversity workflow and templates support various associations, such as those between organisms, between taxa, between taxa and environments, between organisms and nucleotide sequences amongst others. To do this, the domain-specific workflow and templates rely on community-agreed and widely used standards and persistent identifiers and API services from the likes of ChecklistBank, Catalogue of Life, GBIF, GenBank/ENA, BOLD, Darwin Core, ZooBank, Index Fungorum, MycoBank, IPNI and TreatmentBank.</p> <p><iframe allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/LUukUZFp5lM?si=aDcXYvok5eFwROjZ" title="YouTube video player" width="100%"></iframe></p> </div> </div> </div> <div class="col-md-6 col-xs-12"> <div class="accordion-border"> <div class="row middle-xs accordion-toggle"> <div class="col-xs start-xs">ARPHA Writing Tool (AWT)</div> <div class="col-xs-2 end-xs"><span class="plusminus">+</span></div> </div> <div class="accordion-content"> <p>Being passionate advocates for open science, at Pensoft we have always made sure to not only provide freely accessible digital content, but also encourage collaboration in the peer-review, publication and dissemination process. Thus, we developed the <a href="http://arpha.pensoft.net/" target="_blank">ARPHA Writing Tool</a> (AWT) to allow authors, co-authors, external contributors, pre-submission reviewers, linguistic and copy editors to gather in the intuitive and user-friendly online authoring environment and work together on a manuscript.</p> </div> </div> <div class="accordion-border"> <div class="row middle-xs accordion-toggle"> <div class="col-xs start-xs">Pensoft Taxon Profile (PTP)</div> <div class="col-xs-2 end-xs"><span class="plusminus">+</span></div> </div> <div class="accordion-content"> <p>The web-based harvester Pensoft Taxon Profile (PTP) was developed to automatically harvest information about any biological taxon name mentioned within a publication and link it to external resources, for example <a href="http://www.crossref.org/" target="_blank">CrossRef</a>, <a href="http://ncbi.nlm.nih.gov" target="_blank">PubMedCentral</a>, <a href="http://ncbi.nlm.nih.gov/pubmed" target="_blank">PubMed</a>, <a href="http://www.biodiversitylibrary.org/" target="_blank">Biodiversity Heritage Library</a>, <a href="http://www.ncbi.nlm.nih.gov/genbank/" target="_blank">NCBI/GenBank</a>, <a href="http://zoobank.org/" target="_blank">ZooBank</a>, <a href="http://www.ipni.org/" target="_blank">International Plant Name Index</a> (IPNI), <a href="http://www.indexfungorum.org/names/names.asp" target="_blank">Index Fungorum</a>, <a href="http://www.iucn.org/" target="_blank">International Union for Conservation of Nature</a> (IUCN), <a href="https://en.wikipedia.org/" target="_blank">Wikipedia</a>, <a href="http://eol.org/" target="_blank">Encyclopedia of Life</a>, <a href="http://plazi.org/" target="_blank">Plazi.org</a>, and others. As a result, a dynamic web-page for that taxon name is being created in real time, which saves our readers a great amount of time and efforts.</p> </div> </div> <div class="accordion-border"> <div class="row middle-xs accordion-toggle"> <div class="col-xs start-xs">ReFindit</div> <div class="col-xs-2 end-xs"><span class="plusminus">+</span></div> </div> <div class="accordion-content" style="display: none;"> <p>Led by our desire to provide our users with user-friendly and accessible knowledge, we created a handy literature and data discovery tool, called <a href="http://refindit.org/" target="_blank">ReFindit</a>. In order to access a publication, all you need to do is enter any relevant information, such as a Digital Object Identifier (DOI), author, title, or simply a bit of free text and click a ‘Search’ button. <a href="http://refindit.org/" target="_blank">ReFindit</a> searches and gathers information for you from metadata stored on <a href="http://www.crossref.org/" target="_blank">CrossRef</a>, <a href="https://www.datacite.org/" target="_blank">DataCite</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed" target="_blank">PubMed</a>, <a href="https://www.mendeley.com/" target="_blank">Mendeley</a>, <a href="http://refbank.org/" target="_blank">RefBank</a>, and the<a href="http://globalnames.org/docs/gnub/" target="_blank"> Global Names Usage Bank</a> (GNUB).</p> </div> </div> <div class="accordion-border"> <div class="row middle-xs accordion-toggle"> <div class="col-xs start-xs">Annotator</div> <div class="col-xs-2 end-xs"><span class="plusminus">+</span></div> </div> <div class="accordion-content" style="display: none;"> <p>The <a href="https://annotator.pensoft.net/" target="_blank">Pensoft Annotator</a> is a web application serving to annotate free text with ontology terms from any ontology or vocabulary list. The Annotator is a resource of the <a href="https://annotator.pensoft.net/api" target="_blank">Pensoft API</a> which allows annotation of free text with ontology terms.</p> <p>The Pensoft Annotator was build by Pensoft Publishers to help with the semantic enrichment of published articles. Pensoft is actively working to implement semantics into its publishing process to link taxonomic names, species occurrences, habitats, localities, people, institutions and sequences.</p> </div> </div> </div> </div> </div> </div> <script> $(document).ready(function () { initAccordeon('accordion'); }); </script></div> <div class="wrapper"> <div class="row with100"> <div class="col-md-3 col-xs-12"> </div> <div class="col-md-9 col-xs-12"> </div> </div> </div> </div> </div> <div id="P-General-Popup-Content" class="P-PopUp"></div> <div class="popup-background" style="display:none"></div> <div id="warningCookie" class="warningCookie"> <div class="row arownd-xs middle-xs"> <div class="col-xs center-xs pwt_additional_class"> <p>This website uses cookies in order to improve your web experience. <a href="https://pensoft.net/terms#Cookies" target="_blank">Read our Cookies Policy</a></p> </div> <div class="col-xs-2"> <a id="removeWarningCookie">OK</a> </div> </div> </div> <script 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