Track changes and easy comparison of manuscript versions now available in ARPHA Writing Tool

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.

Track changes

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.

Track_changes_on

 

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.

Track_changes_see_user

 

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.

revision_history_compared

 

Again, newly added text shows in green, while the deleted text is crossed over and appears in red.

Step-by-step instructions on both how to track changes and compare past versions are available in the Tips and Tricks guidelines accessible anytime in the header of the writing tool.  

Tips_and_tricks

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*The open access scholarly journals Biodiversity Data JournalResearch Ideas and Outcomes(RIO Journal), One EcosystemBioDiscovery and Biodiversity Information Science and Standards (BISS) are all making use of the technologically advanced collaboration-centred ARPHA-XML workflow, which features the signature ARPHA Writing Tool.

ARPHA-Proceedings Module: Streamline conference abstracts authoring, editing and publication

Creating, reviewing, editing and publishing of collections of proceedings from conferences, symposia and workshops is now available with the ARPHA-Proceedings module via the publishing platform ARPHA.

Designed as a venue for conference organisers to streamline proceedings publications, while simultaneously giving credit to the authors and preserving their contributions in a format that makes them easy to find and read by both humans and machines, the ARPHA-Proceedings module can be regarded as a simplified and straightforward journal publishing process specialised for conference abstracts.

The workflow supports multiple proceedings collections. For instance, a proceedings publishing platform could be created for a particular conference taking place on a regular basis or for a number of conferences organised by an institution or a society. A fine example is the Proceedings of TDWG dedicated to the yearly Biodiversity Information Standards (TDWG) conference.

Within the platform, hierarchical article collections could also be established. Abstracts can be submitted to sub-collections dedicated to various workshops/symposia within a larger event. The different sub-collections can be handled by different editors, normally the workshop/symposia conveners.

The workflow used in the ARPHA-Proceedings module includes ARPHA Writing Tool, editorial/technical evaluation, publication and dissemination.

At any point and at no additional costs, the platform can be modified to feature additional article types (e.g. full-text papers, posters, talks etc.). It is for the conference organisers to decide whether these submissions are to undergo a conventional peer review process.

Abstracts can be enriched with citations, figures, tables, data and multimedia if the conference organisers decide to allow it.

Abstracts can be published straight on the platform as soon as an editor approves them, so that the publication is available online ahead of the conference.

Abstracts published in this way have all features common for regular articles published via ARPHA, including Digital Object Identifier (DOI); publication in HTML, PDF and machine-readable and harvestable XML; citation, indexing and archiving in various databases; dissemination and others.

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Below you can find a practical guide to the submission process of a conference abstract and assigning it to a collection via the ARPHA-Proceedings module.

1. Log in at the platform’s website or ARPHA Writing Tool.

Home awt

 

2. Click Start a manuscript to see the platform and article type options.

start a manuscript

 

3.  Select a venue and article type for your manuscript.

select platform and article type

4. Click Collections on the navigation bar at the top. This is where you select the conference track to which you are assigning your manuscript (this does not guarantee acceptance in that track).

Collection tab

Select collections track

5. Fill in your abstract’s metadata by hovering over a category, and then clicking on the pencil icon. The fields Title, Abstract, “Keywords”, and Presenting Author are mandatory. The submitting author and affiliation are taken from the profile of the logged-in user. More authors can be added by clicking the icon beside Authors on the left-hand side. The corresponding author and the authors’ order can be changed from the same menu. The corresponding author must be available to communicate about the abstract until final acceptance for publication. The presenting author is the person who will actually be giving the talk/demonstration.

Mandatory fields

6. You may add references, figures, tables (if allowed on the particular platform) by clicking on the appropriate icon. You may also upload supplementary materials associated with the abstract.

figures references etc

7. Click Validate. An automated check will ensure that all mandatory fields are filled in and the abstract is assigned to a collection.

8. When you are ready to submit your abstract, click Submit for technical review. This will send the manuscript to the track editors, who will review it for relevance to the track. The button will be visible as soon as the validation has been successful.

9. The editors of the track to which you have submitted your abstract may accept or reject your submission, send feedback requesting changes or suggest submission to a different track.

10. Once the abstract is accepted, the Submit to the journal button becomes visible in ARPHA Writing Tool. You need to click this button and go through a checklist of submission steps. The fourth and final step asks you to assign categories to your submission (optional). When the submission process is finalised, the abstract goes directly to production and publication, a DOI is assigned and the abstract cannot be further revised.

submit to the journal

11. To see your manuscripts, go to the ARPHA Writing Tool’s website, log in and click the See more button, so that you can access your ARPHA dashboard.

see more in AWT

On the right-hand side, you can see the stage each manuscript is currently at, along with the collection it has been assigned to (note that this does not mean that it has been approved for this collection).

user dashboard

If an abstract is at the Draft stage, it means that it is still being authored. Once submitted for Technical Review, it reaches the In pre-submission review stage where it stays until a Collection editor approves it for addition to a particular collection. In layout means that a manuscript is successfully submitted to the journal and awaiting publication.

12. If at any time you feel in need for further assistance, you can send an email to the journal’s technical staff via the system. Click Helpdesk on the top navigation bar to open a new window with an email form for you to fill in.

Helpdesk

Please keep in mind that the stepwise instructions displayed are subject to slight modifications per request. Feel welcome to contact us with your personal platform’s needs!

Faster, Better, Stronger: New batch of updates now available in ARPHA Writing Tool

Only a couple of months ago, we announced a whole set of exciting features newly applied to ARPHA Writing Tool, based on the feedback we received from our users. Now, we are delighted to announce that we are back with a fresh batch of updates.

Here’s what we recently got in store for all authors in Research Ideas and Outcomes (RIO), Biodiversity Data JournalOne Ecosystem and BioDiscovery, all powered by the innovative end-to-end journal publishing platform ARPHA and making use of the new-age ARPHA Writing Tool:

  • We have become faster. ARPHA has been optimised, so that it is even easier to prepare your manuscript. Enjoy your references and whole datasets being delivered straight into your draft in the blink of an eye!
  • Speaking of references, we have updated our Reference Parser. Simply copy-paste a reference in the box and click Parse – ARPHA Writing Tool will have it ready to go on your list momentarily!      

parser

 

parser2

 

  • Yet, there’s even more to the reference-related updates! To double-check an in-text citation in your manuscript, all you need to do is hover over it to see the full-text reference it is linked to.

hover

 

  • Our new toolbar and re-arranged functionalities make up for the better intuitivity of the ARPHA Writing Tool that welcomes you the moment you open a new manuscript.

toolbar2

 

  • Hover over the new toolbar and you will notice another new perk we have added for your convenience. Keyboard shortcuts are now implemented to the ARPHA Writing Tool to let you add smart objects as you type.
  • Get a stronger grip on your figures! Two new buttons let you re-order your figures either by number, or by order of appearance. Alternatively, enter editing mode and simply drag and drop any figure wherever you wish.

drag and drop figures

 

We thank you for your continuous feedback which helps us focus on tailoring the ARPHA Writing Tool according to the needs and taste of our clients.

We are already working hard on the next updates, so keep an eye on us!

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In the meantime, please feel welcome to test our new features and let us know what you think. We will be happy to address any comments and requests on info@arphahub.com.

The 5 Most Distinct Features of ARPHA

Authoring, Reviewing, Publishing, Hosting and Archiving, this is what stands behind the innovative and fully integrated journal publishing solution ARPHA. This end-to-end platform not only puts all stages of the publishing process in one place for the first time, but also allows users to choose from a full set of accompanying services.

But what makes it really stand out? Here are the five most distinct features which make ARPHA unique:

Feature 1
Two journal publishing workflows: ARPHA-XML & ARPHA-DOC

Aiming at flexibility, ARPHA gives a choice between two interconnected but independently functioning publishing workflows that journals and publishers can choose between or use in combination:

  • ARPHA-XML: Entirely XML- and Web-based collaborative authoring, peer review, production and publication workflow, made possible via the innovative ARPHA Writing Tool.
  • ARPHA-DOC: Document-based submission, peer review, production and publication workflow.

Not only do users have the freedom to choose what suits their needs best, but they also get the options to effortlessly upgrade to our XML, entirely web-based workflow at a later stage, due to the high integration and automatisation of processes within ARPHA.

picture1

Feature 2
No just a software platform, it comes with a full range of services to choose from

ARPHA is not just a software that you download! This highly integrated publishing solution offers its end-to-end platform, in combination with a full range of accompanying servicesthat you can pick & mix to get a final product adjusted to your needs.

 

services

Feature 3
White-label publishing, all the benefits of ARPHA under your imprint

Developed and tested in-house by scientific publisher Pensoft, ARPHA now comes as a stand-alone brand and offers a completely white-label publishing option for journals and publishers. You can enjoy all the benefits of having ARPHA as the backbone of your journal or collection of journals, while at the same time continue publishing under your own imprint.

Moreover, switching to ARPHA guarantees you an upgrade of your visual identity by offering dedicated web-design and setup services for your new journal website or publishing platform. For example, having recently moved to ARPHA, the Lithuanian VGTU Press journal Business Theory and Practice enjoys a brand new, individually designed website. While the journal has the ARPHA Platform as its backbone, it remains a completely separate entity published on behalf of VGTU Press.

 

btp

Feature 4
High-level integration via web services & data exchange

ARPHA is fully integrated with all leading indexing and archiving services. Our partners include CrossRef, Zenodo, Open Ayre, PubMed Central and DOAJ, to name just a few.

The full automatisation of processes within ARPHA means that all content is directly exported upon publication and without any extra human effort. This means that publishers and Editors-in-Chief can sit back and relax after pressing the “publish-an-article button”, while ARPHA makes sure that all their content is safely archived and successfully disseminated.

partners

Feature 5
Flexibility at each step of tailoring your publishing model

One of the greatest assets of ARPHA is its flexibility, when it comes to tailoring the best service for each individual client. While deciding what suits their needs, publishers and Editors-in-Chief get to choose from a full range of options at each step of the publishing cycle.

Starting from the branding model and tailored web design, through input types, peer review options and publication outputs, and finishing with your preferred revenue model, ARPHA offers a number of possibilities at each step to let you customise a platform that works for your journals at an affordable price.

 

pub-models

 

ARPHA is a home to several flagship journals, such as Research Ideas and Outcomes (RIO) Journal (SPARC Innovation Award Winner for 2016)ZooKeys, Biodiversity Data Journal and others.You may also find some concise information about ARPHA in this flyer.

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Would you be interested to set up a call for a brief demo? Please do not hesitate to contact us at info@arphahub.com if you wish to explore opportunities to use ARPHA as a new home for your journal!

Import of Specimen or Occurrence Records Into Taxonomic Manuscripts

Repositories and data indexing platforms, such as GBIFBOLD systems, or iDigBio hold documented specimen or occurrence records along with their record ID’s. In order to streamline the authoring process, save taxonomists’ time, and provide a workflow for peer-review and quality checks of raw occurrence data, the ARPHA team has introduced an innovative feature that makes it possible to easily import specimen occurrence records into a taxonomic manuscript (see Fig. 1).

For the remainder of this post we will refer to specimen data as occurrence records, since an occurrence can be both an observation in the wild, or a museum specimen.

Figure1

Fig. 1: Workflow for directly importing occurrence records into a taxonomic manuscript.

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 GBIFBOLD systems, or iDigBio, 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 prepared in the ARPHA Writing Tool. The import functions as follows:

  1. the author locates an occurrence record or records in one of the supported data portals;
  2. the author notes the ID(s) of the records that ought to be imported into the manuscript (see Fig. 2, 3, and 4 for examples);
  3. the author enters the ID(s) of the occurrence records in a form that is to be seen in the materials section of the species treatment, selects 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 (see Fig. 5).

Figure 2       Figure 3

Fig. 2: (Left) An occurrence record in iDigBio. The UUID is highlighted; Fig. 3: (Right) An occurrence record in GBIF. The GBIF ID and the Occurrence ID is highlighted. (Click on images to enlarge)

Figure 4       Figure 5

Fig. 4: (Left) An occurrence record in BOLD Systems. The record ID is highlighted.; Fig. 5:  (Right) All occurrence records corresponding to a OTU. The BIN is highlighted. (Click on images to enlarge)

We will illustrate this workflow by creating a fictitious treatment of the red moss, Sphagnum capillifolium, in a test manuscript. Let’s assume we have started a taxonomic manuscript in ARPHA and know that the occurrence records belonging to S. capillifolium can be found in 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. 6). When we scroll all the way down in the pop-up window, we see the form which is displayed in the middle of Fig. 1.

Figure 6

Fig. 6: Edit materials.

From here, the following actions are possible:

  • insert (an) occurrence record(s) from iDigBio by specifying their UUID’s (universally unique identifier) (Fig.2);
  • insert (an) occurrence record(s) from GBIF by entering their GBIF ID’s (Fig.3);
  • insert (an) occurrence record(s) from GBIF by entering their occurrence ID’s (note that unfortunately not all GBIF records have an occurrence ID, which is to be understood as some sort of universal identifier) (Fig. 3);
  • insert (an) occurrence record(s) from BOLD by entering their record ID’s (Fig. 4);
  • insert a set of occurrence records from BOLD belonging to a BIN (barcode index number) (Fig. 5).

In this example, select the fifth option (iDigBio) and type or paste the UUID b9ff7774-4a5d-47af-a2ea-bdf3ecc78885 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. 6). The same workflow applies also to the aforementioned GBIF and BOLD portals.

Figure 7

Fig. 7: Materials after they have been imported.

This workflow can be used for a number of purposes but one of its most exciting future applications is the rapid re-description of Linnaean species, or new morphological descriptions of species together with DNA barcode sequences (a barcode is a taxon-specific highly conserved gene that provides enough inter-species variation for statistical classification to take place) using the  Barcode Identification Numbers (BIN’s) underlying an Operational Taxonomic Units (OTU). If a taxonomist is convinced that a species hypothesis corresponding to OTU defined algorithmically at  BOLD systems clearly presents a new species, then he/she can import all specimen records associated with that OTU via inserting that OTU’s BIN ID in the respective fields.

Having imported the specimen occurrence records, the author needs to define one specimen as holotype of the news species, other as paratypes, and so on. The author can also edit the records in the ARPHA tool, delete some, or add new ones, etc.

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 and iDigBio. 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.

Additional Information:

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. 542241.