Monitoring the progress of your manuscript has never been easier!
The eagerly anticipated Track changes feature is now available in ARPHA Writing Tool to further facilitate collaborative authoring in the five academic journals* which currently make use of the ARPHA-XML publishing workflow.
Having tapped into ARPHA’s users constructive feedback, we have also updated our Revision History feature. Now, not only can authors access any past version, as created by their co-authors and collaborators, but they can also compare any two of these at the click of a button.
To let co-authors and collaborators easily see any changes they have made, a user needs to simply switch on the Track changes mode. From now on, each individual author’s input will be highlighted to draw the attention of the next user.
Logically, any newly inserted text will appear in green, while the deleted one will be coloured in red. A hover over a highlighted text will show the user who has made the edit.
To make overseeing even a single edit impossible, ARPHA Writing Tool has made it mandatory for a user to resolve all suggested changes before either submitting the manuscript or switching off the Track changes mode.
Not overlooking any new input, regardless of the length and complexity of a manuscript, is made even easier thanks to the Prev and Next buttons allowing a user to go through the changes one by one.
But what shall you do if you or your co-authors/collaborators happen to forget to switch on the Track changes mode?
Compare Manuscript Versions
Our latest update to the Revision history button lets users compare any two past manuscript versions, so that they can see at a glance what has changed between any two set points in time.
Just like before, clicking the Revision history button delivers a list of all manuscript versions along with the users who have created them in a chronological order. Now, however, a tick box next to each of these allows the user to select any two versions and see all edits that have taken place in between.
Again, newly added text shows in green, while the deleted text is crossed over and appears in red.
Following the launch of our self-developed journal publishing platform ARPHA (standing for Authoring, Reviewing, Publishing, Hosting and Archiving, all happening at one place), we were so happy with the outcome, that we couldn’t help sharing it with the world. Therefore, it’s on offer not only to our own journals and authors, but it’s also at hand to journals looking for their new home. Just let us know you’re interested!
On these lines, what could be a better place to have a chat about the transition in scholarly publishing, open science, research reproducibility and, of course, the advantages of having a journal published on ARPHA, than Frankfurt Book Fair 2016? Between 18th and 23rd October, this immense event will be all about unveiling and celebrating the evolution in the publishing industry, with exhibitors, trade and private visitors from across the globe, gathering together, led by their common expertise and passion.
Meet us at HotSpot Professional and Scientific Information Stage, Hall 4.2, Stand M90, during the Fair, and make sure you don’t miss the “ARPHA: Next-Generation Journal Publishing” presentation at 11:30 AM (local time) on Friday, 21st October, where Pensoft’s Founder and Managing Director Prof Lyubomir Penev will shed more light on the first end-to-end publishing solution, providing everything a journal needs in a technologically advanced, highly efficient and user-friendly manner.
ARPHA in a few notes:
With ARPHA you can choose between two journal publishing workflows: ARPHA-DOC and ARPHA-XML. The former provides document-based submission for the articles in a journal, as well as peer review and publication. The latter makes use of the ARPHA Writing Tool, which takes all processes, including authoring, peer review and post-publication updates, to an online environment, created with collaboration and openness in mind.
ARPHA takes care of all the steps that go along with academic publishing and its efficient dissemination, so that it provides a long list of perks to make it easier for the scientific community to bring research to light. Website design, online editorial management system, linguistic editing, semantic markup, promotion and (sub-)article usage metrics are only a part of the services the platform has to offer.
The publishing models
ARPHA basically lets users mix-and-match services and features to create the publishing model that’s the best fit for their journals. How do you envision your imprint / web-design look / manuscript input / peer review process / publication output / revenue model? ARPHA understands your journal’s individual needs and works around them.
Find out more about ARPHA at our talk, or come and meet us at our stand in HotSpot Professional and Scientific Information (Hall 4.2, M90).
Based on our earlier post, we will now go through our latest updates and highlight the new features that have been added since then.
Repositories and data indexing platforms, such as GBIF, BOLD systems, iDigBio, or PlutoF, hold, among other types of data, specimen or occurrence records. It is now possible to directly import specimen or occurrence records into ARPHA taxonomic manuscripts from these platforms [see Fig. 1]. We’ll refer to specimen or occurrence records as simply occurrence records for the rest of this post.
Until now, when users of the ARPHA writing tool wanted to include occurrence records as materials in a manuscript, they would have had to format the occurrences as an Excel sheet that is uploaded to the Biodiversity Data Journal, or enter the data manually. While the “upload from Excel” approach significantly simplifies the process of importing materials, it still requires a transposition step – the data which is stored in a database needs to be reformatted to the specific Excel format. With the introduction of the new import feature, occurrence data that is stored at GBIF, BOLD systems, iDigBio, or PlutoF, can be directly inserted into the manuscript by simply entering a relevant record identifier.
The functionality shows up when one creates a new “Taxon treatment” in a taxonomic manuscript in the ARPHA Writing Tool. To import records, the author needs to:
Locate an occurrence record or records in one of the supported data portals;
Note the ID(s) of the records that ought to be imported into the manuscript (see Tips and Tricks for screenshots);
Enter the ID(s) of the occurrence record(s) in a form that is to be seen in the “Materials” section of the species treatment;
Select a particular database from a list, and then simply clicks ‘Add’ to import the occurrence directly into the manuscript.
In the case of BOLD Systems, the author may also select a given Barcode Identification Number (BIN; for a treatment of BIN’s read below), which then pulls all occurrences in the corresponding BIN.
We will illustrate this workflow by creating a fictitious treatment of the red moss, Sphagnum capillifolium, in a test manuscript. We have started a taxonomic manuscript in ARPHA and know that the occurrence records belonging to S. capillifolium can be found on iDigBio. What we need to do is to locate the ID of the occurrence record in the iDigBio webpage. In the case of iDigBio, the ARPHA system supports import via a Universally Unique Identifier (UUID). We have already created a treatment for S. capillifolium and clicked on the pencil to edit materials [Fig. 2].
In this example, type or paste the UUID (b9ff7774-4a5d-47af-a2ea-bdf3ecc78885), select the iDigBio source and click ‘Add’. This will pull the occurrence record for S. capillifolium from iDigBio and insert it as a material in the current paper [Fig. 3].
This workflow can be used for a number of purposes. An interesting future application is the rapid re-description of species, but even more exciting is the description of new species from BIN’s. BIN’s (Barcode Identification Numbers) delimit Operational Taxonomic Units (OTU’s), created algorithmically at BOLD Systems. If a taxonomist decides that an OTU is indeed a new species, then he/she can import all the type information associated with that OTU for the purposes of describing it as a new species.
Not having to retype or copy/paste species occurrence records, the authors save a lot of efforts. Moreover, they automatically import them in a structured Darwin Core format, which can easily be downloaded from the article text into structured data by anyone who needs the data for reuse.
Another important aspect of the workflow is that it will serve as a platform for peer-review, publication and curation of raw data, that is of unpublished individual data records coming from collections or observations stored at GBIF, BOLD, iDigBio and PlutoF. Taxonomists are used to publish only records of specimens they or their co-authors have personally studied. In a sense, the workflow will serve as a “cleaning filter” for portions of data that are passed through the publishing process. Thereafter, the published records can be used to curate raw data at collections, e.g. put correct identifications, assign newly described species names to specimens belonging to the respective BIN and so on.
The work has been partially supported by the EC-FP7 EU BON project (ENV 308454, Building the European Biodiversity Observation Network) and the ITN Horizon 2020 project BIG4 (Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs), under Marie Sklodovska-Curie grant agreement No. 642241.