Virtual Biodiversity ViBRANT 3 in 1: The Pensoft Writing Tool (PWT) Lyubomir Penev, Pavel Stoev, Teofor Georgiev Pensoft Publishers [email protected] ViBRANT

Virtual BiodiversityViBRANT

3 in 1: The Pensoft Writing Tool (PWT)

Lyubomir Penev, Pavel Stoev, Teofor Georgiev

Pensoft [email protected]

ViBRANTVirtual Biodiversity

Workpackage 6Scholarly Publishing


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PWT aims and functionalities

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PWT combines: (1) writing of a taxonomic manuscript; (2) upfront markup of the text, and (3) submission to an appropriate journal into one and the same process (tool)

PWT is a core module of the forthcoming Biodiversity Data Journal (BDJ) and links formatted manuscript to the Pensoft Online Editorial System by a push-button

Provides opportunity for publishing any kind of biodiversity data in the form of short taxonomic treatments or even single nomenclatural acts, as well as single records, biology observations, local checklists, etc.

Conventionally structured biodiversity papers (taxonomic reviews, revisions, checklists, phylogenies, etc) can be written and submitted through the PWT as well

Module which will accept taxonomic treatments generated from Scratchpads, and other platforms


PWT facilitates writing of manuscripts by

Predefined templates for different types of manuscripts (e.g. single taxonomic treatments, nomenclatural acts, checklists, software descriptions, data papers)

Automated, pre-prublication registration of nomenclatural acts (IPNI, IF, ZooBank) and automated release of names on the day of publication

Automated checking of availability of names in external databases (e.g., GNI, ION, etc.)

Automated integration of datasets into the text through accepted standards, such as Darwin Core (occurrence data, taxon checklists, material citations) NLM (references)

Automated search in external reference databases (Pensoft Literature Database, Mendeley, Citebank, etc.) and import of references into the manuscript

Cross-checking and cross-referencing between the in-text citations and reference lists

Creation of Custom fields at various levels

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PWT general characteristics

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Based on TaxPub XML schema, an extension to the Document Type Definitions (DTD) of the US NLM Tag Suite

Occurrence and material description data structured after the TDWG DarwinCore Schema

Compliant with the Fourth edition of the ICZN (2000) and the Vienna Code (ICBN 2006)

Reflects the specifics of the two codes and the recent alterations of the ICBN (ICNafp)

Projected on the basis of and compliant with the Zoological Record terminology

Draft BioCode was also consulted

PWT deals with all extant and extinct organism groups

Taxonomic Backbone based on and compliant with the COL/GBIF classification

PWT Taxon Treatment module treats taxa of any taxonomic rank


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Taxon treatments: general description and specifics

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Two types of treatments sensu lato: nomenclatural (new taxa, new taxonomic alterations) and non-nomenclatural (new records, re-descriptions, etc.)

The general structure of a taxon treatment is similar for all organism groups but reflects the specifics of the different groups, the nomenclature codes and terms

The Taxon treatments for extinct taxa (regardless animals or plants) comprise Geological Contents Section in addition to the other sections

There are also differences in the Taxon treatments of Animalia and Protista, e.g. the presence of nomenclatural term “hapantotype” in latter group


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Nomenclatural and taxonomic acts: main classes at treatment level

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New taxon (regardless the rank, sp.n., gen.n., fam.n., etc.) OK FOR BOTH ICBN AND ICZNNew synonym (syn.nov, senior synonym) (OK FOR BOTH CODES; not a separate tretament in botany! Stays separate treatment in zoology)Removal from synonymy (should it exist separately or be listed under “resurrected name”?) (OK FOR BOTH CODES. NOT a separate treatment. Stays separate treatment in zoology))Resurected name (nomen resurrectum = removal from synonymy or = revalidated combination; should it be listed as a separate nomenclatural act or only as a phrase-level characteristics of a name?) TO ERASE THIS CATEGORY; OVERLAP WITH EITHER REMOVAL FROM SYNONYMY OR NEW COMBINATION)New name (nomen novum) GOES UNDER REPLACEMENT NAME IN BOTANY; IN ZOOLOGY IT IS A PARTICULAR CASE OF REPLACEMET NAME; goes as a dropbox option under “Name replacement”Replacement name (existing name proposed as replacement name) (= nomen resurrectum?? = revalidated combination??) (OK FOR BOTH CODES)New combination (comb. nov.) (OK FOR BOTH CODES)Revalidated combination (comb. revalid.) (does it overlap completely with name resurrection?) (NOT IN BOTANY – IPNI use only “new combination”); RARELY USED IN ZOOLOGY, NOT COMMON! In Zoology ot will come in a dropbox option under New combinationStatus change (raised to/from; downgraded to/from) (OK FOR BOTH CODES, IN BOTANY NOT SEPARATED< GOES UNDER NEW COMBINATION)Type designation (at species and supraspecific level; lectotype, neotype, epitype, type species, type genus) (OK FOR BOTH CODES)


Nomenclatural term at phrase level (nomen)

abortivumalternativum ambigua available (ICZN)combinatio confusum conservandum (conserved name)correctum dubium illegitimum (equiv. to not avialable)imperfectuminvalidum Inviolatumlegitimatumnegatum novum (exists also at treatment level) (in botany reeplacement name is preferred)replacement name (exists also at treatment level)

nudum nullum oblitum oppressum (for works not for name., rarel used)perfectrumprotectumprovisorium rejiciendum (rejected name, used in botany)sanctioned name (mycology)subnudum (ICBN) (try to get rid of that)superfluum (ICBN) (used quite a lot)translatumvanumvetitumvalid (ICBN ) (= validly published)Species inquirenda (NOT in botany)

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1. To evaluate the general design of the PWT from the viewpoint of user-friendliness

2. To evaluate/correct the main classes of nomenclatural acts and taxon treatments from the viewpoint of practicing taxonomists and especially taxonomic editors (IPNI, IF)

3. To propose additional treatments types that could extend the usability of PWT

4. To discuss the technical and semantic integration with Scratchpads and other platforms

The goals of the present workshop


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Acknowledgements

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Nigel Robinson, Zoological Record, for providing the list of nomenclatural acts and termsPaul Kirk, Index Fungorum, for the first comments on the template designDavid Roberts, ViBRANT, for the help in organizing this workshop

ViBRANT


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Presence of basionym section in e.g., new genus description based on previously described species, designation of lecto- or neotype, etc.

Presence of specific nomenclatural acts (e.g. epitype designation, tautonymy)

Presence of specific nomenclatural terms: isoparatype, isolectotype, isoneotype, isosyntype, isotype

While the Taxon treatmens for new species-level taxa of animals comprise only species and subspecies ranks in those dealing with plants there are also categories below subspecies, e.g. variety, form, cultivar, etc.

Specifics for the taxon treatments for plants

Documents

Virtual Biodiversity ViBRANT 3 in 1: The Pensoft Writing Tool (PWT) Lyubomir Penev, Pavel Stoev, Teofor Georgiev Pensoft Publishers [email protected] ViBRANT