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Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing

November 2022
Research Ideas and Outcomes 8:97374

DOI:10.3897/rio.8.e97374

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Authors:

Donat Agosti

Plazi

Laurence Bénichou

Muséum National d'Histoire Naturelle

Wouter Addink

Naturalis Biodiversity Center

C. Arvanitidis

Hellenic Centre for Marine Research

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The paper summarises many years of discussions and experience of biodiversity publishers, organisations, research projects and individual researchers, and proposes recommendations for implementation of persistent identifiers for article metadata, structural elements (sections, subsections, figures, tables, references, supplementary materials and others) and data specific to biodiversity (taxonomic treatments, treatment citations, taxon names, material citations, gene sequences, specimens, scientific collections) in taxonomy and biodiversity publishing. The paper proposes best practices on how identifiers should be used in the different cases and on how they can be minted, cited, and expressed in the backend article XML to facilitate conversion to and further re-use of the article content as FAIR data. The paper also discusses several specific routes for post-publication re-use of semantically enhanced content through large biodiversity data aggregators such as the Global Biodiversity Information Facility (GBIF), the International Nucleotide Sequence Database Collaboration (INSDC) and others, and proposes specifications of both identifiers and XML tags to be used for that purpose. A summary table provides an account and overview of the recommendations. The guidelines are supported with examples from the existing publishing practices.

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Research Ideas and Outcomes 8: e97374

doi: 10.3897/rio.8.e97374

Reviewable v 1

Guidelines

Recommendations for use of annotations and

persistent identifiers in taxonomy and

biodiversity publishing

Donat Agosti , Laurence Benichou , Wouter Addink , Christos Arvanitidis , Terence Catapano , Guy

Cochrane , Mathias Dillen , Markus Döring , Teodor Georgiev , Isabelle Gérard , Quentin Groom ,

Puneet Kishor , Andreas Kroh , Jiří Kvaček , Patricia Mergen , Daniel Mietchen , Joana Pauperio ,

Guido Sautter , Lyubomir Penev

‡ Plazi, Bern, Switzerland

§ Museum national d'Histoire naturelle, Paris, France

| CETAF, Brussels, Belgium

¶ Naturalis Biodiversity Center, Leiden, Netherlands

# Distributed System of Scientific Collections - DiSSCo, Leiden, Netherlands

¤ LifeWatch ERIC, Seville, Spain

« European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton,

Cambridge, United Kingdom

» Meise Botanic Garden, Meise, Belgium

˄ GBIF, Copenhagen, Denmark

˅ Catalogue of Life, Leiden, Netherlands

¦ Pensoft Publishers, Sofia, Bulgaria

ˀ Royal Museum for Central Africa, Tervuren, Belgium

ˁ Naturhistorisches Museum, Vienna, Austria

₵ National Museum Prague, Prague, Czech Republic

ℓ Leibniz Institute of Freshwater Ecology and inland Fisheries, Berlin, Germany

₰ European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom

₱ KIT / Plazi, Karlsruhe, Germany

₳ Institute of Biodiversity & Ecosystem Research - Bulgarian Academy of Sciences, Sofia, Bulgaria

Corresponding author: Lyubomir Penev (l.penev@pensoft.net)

Received: 09 Nov 2022 | Published: 15 Nov 2022

Citation: Agosti D, Benichou LL, Addink W, Arvanitidis C, Catapano T, Cochrane G, Dillen M, Döring M,

Georgiev T, Gérard I, Groom Q, Kishor P, Kroh A, Kvaček J, Mergen P, Mietchen D, Pauperio J, Sautter G,

Penev L (2022) Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity

publishing. Research Ideas and Outcomes 8: e97374. https://doi.org/10.3897/rio.8.e97374

Abstract

The paper summarises many years of discussions and experience of biodiversity

publishers, organisations, research projects and individual researchers, and proposes

‡ §,| ¶,# ¤ ‡

« » ˄,˅¦ˀ»

‡ˁ ₵ ˀ,» ℓ₰

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4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are

credited.

recommendations for implementation of persistent identifiers for article metadata, structural

elements (sections, subsections, figures, tables, references, supplementary materials and

others) and data specific to biodiversity (taxonomic treatments, treatment citations, taxon

names, material citations, gene sequences, specimens, scientific collections) in taxonomy

and biodiversity publishing. The paper proposes best practices on how identifiers should

be used in the different cases and on how they can be minted, cited, and expressed in the

backend article XML to facilitate conversion to and further re-use of the article content as

FAIR data. The paper also discusses several specific routes for post-publication re-use of

semantically enhanced content through large biodiversity data aggregators such as the

Global Biodiversity Information Facility (GBIF), the International Nucleotide Sequence

Database Collaboration (INSDC) and others, and proposes specifications of both identifiers

and XML tags to be used for that purpose. A summary table provides an account and

overview of the recommendations. The guidelines are supported with examples from the

existing publishing practices.

Keywords

semantic publishing, taxonomy publishing, semantic annotation, biodiversity, persistent

identifiers, taxa, specimens, sequences, treatments, XML, JATS, TaxPub, tagging

Introduction

Specifics of taxonomic publications

Deans et al. (2012) very elegantly stated that “Taxonomists are arguably the most active

annotators of the natural world, collecting and publishing millions of phenotype data

annually through descriptions of new taxa. By formalising these data, preferably as they

are collected, taxonomists stand to contribute a data set with research potential that rivals

or even surpasses genomics”.

Taxonomic publications communicate the discovery of new biological taxa or new data on

already known taxa in the form of taxonomic treatments, well delimited sections of text for

each taxon (Fig. 1; Catapano 2010, Penev et al. 2011, Agosti and Egloff 2009, Agosti and

Egloff 2021). New research results are added to the already existing treatments by citing

previous treatments using a “treatment citation”. Altogether, the treatments and data

related to them represent the basis for the knowledge graph on the Earth’s biological

diversity. Treatments have been used from the beginning of modern taxonomy by Linnaeus

in 1753 for plants and in 1758 for animals (Linnæus 1753, Linné 1758). Treatments begin

with a nomenclature section including a unique identifier for the taxonomic name, the Latin

Binomen for species or Latin Name for a supraspecific taxon such as genus, family or

order. This is followed by one or more sections covering the citation of previous treatments

of the same taxon, description, diagnosis, etymology, distribution, material citations or

conservation. New taxa are based on type and other specimens in natural history

collections and data on these specimens are included in the treatment in the form of

2Agosti D et al

dedicated “material citations”. This new style of presenting information on biological taxa

required a certain degree of comprehension and adoption but was widely accepted by the

taxonomists in the second half of 18th century.

Translated into today’s digital world, this simple framework of presenting biological taxa in

both human readable and machine interpretable format is sufficient, given that it is present

as digital accessible knowledge (DAK, Fawcett et al. 2022), to build a knowledge graph of

the Earth’s biological diversity. By “machine readable” we mean that the data are

structured systematically so that computers can be programmed to process and interpret

the data. This requires that the elements taxonomic treatment, taxonomic name, treatment

citation, material citation and other important terms of relevance are annotated in

publications following a community accepted standard, and are made citable through

inclusion of the respective identifiers of the cited elements (e.g., treatment in treatment

citations, taxonomic name, specimens or digital specimen for the material citations). Thus

to explore known biodiversity, this is the minimal degree of digital accessible knowledge

needed to allow us to ask questions such as “What do I know about taxon X?”, “What are

the synonyms of a taxonomic name?”, and “What are the facts used to make the

changes?”.

Research results presented in the biodiversity literature are one of the best curated data

(Deans et al. 2012) providing expert linking of taxonomic names, molecular, including

omics data, phenomics data, specimens, geographical, environmental and climatic data,

taxonomies and phylogenies, previously published data, publications and people via

accession codes, material citations, treatment citations, bibliographic references or

personal identifiers, respectively. The semantic annotation or semantic role labelling (e.g.

Walls et al. (2014)) of texts, provides an additional feature for identifying the role of people

and taxonomic names. For example, a person mentioned in a material citation can be

Figure 1.

Schematic representation of the taxonomic treatment of Apis mellifera Linnaeus, 1758.

Sources: text: https://doi.org/10.5962/bhl.title.542; figures: https://linnean-online.org/16019/;

composite: https://doi.org/10.5281/zenodo.5168465.

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 3

inferred to be a collector, whereas a person's name in a taxonomic name indicates the role

of authority of the taxon’s name, and an author of the publication in which the taxonomic

name has been published. A taxonomic name in the nomenclature section functions as a

label for the treatment, while a taxonomic name in the treatment body outside the

nomenclature section indicates some sort of connection between the two taxa.

In today’s digital arena these structured texts are an ideal prerequisite to enhance the

publications by making them readable or even machine actionable (Chester et al. 2019).

This includes making, for example, treatments and figures open, findable, accessible,

interoperable and reusable (FAIR) digital objects* , then adding persistent identifiers to the

cited materials, gene sequences, and authors, and annotating them to add a semantic

meaning to those tokens. The use of persistent identifiers is intended for many purposes,

including building a knowledge graph, understanding the use of specimens and their

collections in research, to give credit to individual scientists and institutions, and more

broadly to allow reuse by aggregators, such as the Global Biodiversity Information Facility

(GBIF) or ChecklistBank. Persistent identifiers also contribute to mitigating the taxonomic

impediment recognized by conservation policy (Abrahamse et al. 2021), create new

knowledge management systems, and bridge gaps between different domains such as

taxonomy, ecology and molecular biology in the life sciences. The first working examples of

knowledge graphs in the biodiversity realm are OpenBiodiv (Senderov et al. 2018, Penev

et al. 2019, Dimitrova et al. 2021), Ozymandias (Page 2019) and Synospecies (Gmür and

Agosti 2021).

Use of identifiers

An identifier (ID) is a label for any subject, conceptual, physical or digital

(Dillen et al. 2021). An ID can be called persistent (PID) (Directorate-General for Research

and Innovation (European Commission) et al. 2020) if it can be maintained as a label in the

longer term, in spite of any changes to the subject itself. For example, IDs for people can

be persistent even if their name(s) change or they move to another location or change

jobs. Hence, an ID aims to disambiguate the entity it relates to. To be a PID, it also

needs to be Globally Unique, Persistent and Resolvable (GUPRI, Directorate-General for

Research and Innovation (European Commission) et al. 2020). It should thus be unique at

the context in which it is used and come with a system that maintains the link between the

ID and its subject. For example, in the case of resolvable Uniform Resource Identifiers

(URIs), this system is the internet’s Domain Name System (Hyam et al. 2012). However, it

is still up to the organisation that mints the URI to ensure it remains persistent, as Domain

Names are not. Digital Object Identifiers (DOIs) are another example, making use of the

Handle system to maintain the link between ID and subject. Nevertheless, the onus still

remains on the organisation holding the digital object to ensure that the DOI resolves to the

right object. Technology cannot provide persistency of the identifier, this is an

organisational problem which seems best solved by the creation of consortia of

stakeholders responsible for the PIDs and its metadata. Examples are the DONA

Foundatation, DOI Foundation, ORCID and ROR. PIDs like Handles and DOIs are in place

4Agosti D et al

for about 30 years already which indicates that this way of achieving persistence seems to

work.

As an identifier serves to unequivocally label an entity, it may also be employed to track the

use of it, particularly when that entity is digital. Performance indicators are an important

tool for the efficient management and development of organisations and infrastructures.

Such indicators are used to channel appropriate funding internally, and also to request

funding externally. The more we are able to show the impact and reach of our field, the

easier it is to gather financial support to develop natural history collections, maintain

services, digitise objects and conduct research.

Parallel to the rise of e-publishing, IDs minted and used in biodiversity informatics have

diversified and become increasingly important to link to objects, specimens, and their

digital representation, as well as the component parts of literature (Guralnick et al. 2015,

McMurry et al. 2017, Page 2016, Page 2019, Madden and Woodburn 2021). They form a

scaffold on which to form a biodiversity knowledge graph.

Usage of identifiers can be broad and complex. PIDs are used to identify and link digital

and physical objects or concepts. One of the very first uses of DOIs was identifying

individually published articles as well as references in the bibliographies, which enhanced

the visibility and citability of these articles. DOIs are also used for data and figures, and are

proposed for the digital objects in DiSSCo (Hardisty et al. 2022). For physical specimens in

natural history collections there are the stable HTTP URIs proposed and implemented by

CETAF, also called CETAF stable identifiers (Güntsch et al. 2017) and in Zenodo as

“physical object” (Boschert and Dikow 2022). Likewise, Life Science Identifiers (LSID) were

once used in biodiversity informatics inter alia for concepts (taxonomic names), but in

contrast with e.g. DOIs and ORCIDs were lacking a governance structure to maintain

them, and ORCID or Wikidata identifiers serve as identifiers for people. A PID is needed for

any digital object posted on the Web so it may be easily found, cited, linked, annotated,

and reused. Furthermore, in publications, PIDs and their respective metadata can be

provided for many types of research-related content such as journals, chapters, grants or

funders, datasets, data, text, and images (Guralnick et al. 2015). An emerging consensus

for PIDs is the current development in DiSSCo infrastructure and the BiCIKL project to use

DOIs as community-agreed, unified identifiers for curation of a digital specimen. Digital

specimens will be treated as a FAIR Digital Objects(FDO), that is, as an aggregator of

several existing identifiers of data related to a specimen, such as the identifier for the

physical specimen itself, IDs of material citations of the specimen published in the

literature, IDs of gene sequences from the specimen (INSDC accession codes) and others

(Hardisty et al. 2021).

The Internet’s world wide coverage clearly makes it evident that globally unique identifiers

are a prerequisite to locate the cited resources, and, consequently, through conversion and

transformation of data, to build a knowledge graph, where all these resources can be

identified and linked to each other through their PIDs. Since digitization of objects (e.g., an

article) can occur in parallel, this can lead to collision between identifiers for physical

objects, or across domains, between articles or specimens. Identifiers of different kinds

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 5

have a long tradition in biodiversity research — they served specific purposes such as to

label specimens from an expedition or a natural history collection, and have been

understandable within their respective context. These identifiers served internal

purpose

and therefore only had the requirement to be locally unique. They are not resolvable

through the internet making them hard to use by non-specialists or machines, as you will

need to know the format to interpret them and there is no way to know if they are correct

when used outside their source system. Assigning PIDs resolves these problems but

introduces new challenges: the global uniqueness and opaque string requirements for

persistence makes them hard to use for humans. Therefore additional IDs/labels for usage

by humans, not necessarily globally unique, is also needed, which is not a problem as long

as these are not used for data linkage. However, this will require look-up tables linking

historic identifiers with the respective PIDs or extending non-unique IDs with a prefix to

make it unique. Ideally the connection between the legacy ID and the unique PID is made

either at the metadata level of each object, or within the specimen record (material citation)

in publications.

Because of the current transitional period of digitising biodiversity data, new and different

kinds of PIDs might be minted for the same object. To connect different PIDs for the same

object we will need a discovery mechanism to build look-up tables. The different data

accessible via the resolution of the PIDs will then provide complementary, sometimes

conflicting data about the same objects (such as is discovered by GBIF’s clustering

mechanism* for seemingly similar occurrences) and thus increase the knowledge about

an object.

To minimise the costs of the significant and non-trivial effort of disambiguation of entities

and building and maintaining look-up tables, the recommendations in this paper strongly

encourage the use of harmonised PIDs that are compliant with a community accepted

standard across different journals and publishers and serve, therefore, multiple scientific

disciplines or domains. A good basis for harmonisation, for example, are the

recommendations of the European Open Science Cloud (EOSC) for the use of PIDs that

should be taken into account (Directorate-General for Research and Innovation (European

Commission) et al. 2020, Directorate-General for Research and Innovation (European

Commission) 2020).

On the need of harmonisation

The recommendations in this paper are produced collaboratively by several organisations,

research projects and biodiversity scientists. They are based on nearly 15 years of

experience on annotating unstructured legacy publications by Plazi

(Agosti and Egloff 2009), and on TaxPub XML-based structured publishing by Pensoft,

including 38 journals since 2010 (Penev et al. 2010* ). Furthermore, during several EU-

funded projects such as pro-iBiosphere, EU BON, and COST Mobilise, the focus of

discussions was on building an infrastructure to provide FAIR data, for example, the

Biodiversity Literature Repository (BLR) as well as on the implementation of persistent

identifiers in article XMLs of Plazi and Pensoft (Catapano 2010, Penev et al. 2010, Penev

6Agosti D et al

et al. 2011). Finally, part of this discussion was carried out in the CETAF e-publishing

group’s ongoing work on unique identifiers.

The paper has been largely elaborated and finalised in a collaboration between several

partners in the Biodiversity Community Integrated Knowledge Library project (BiCIKL)

(Penev et al. 2022). In a similar fashion to the harmonisation of PIDs that the Research

Organisation Registry (ROR), Datacite, Crossref and ORCID have agreed (Demeranville et

al. 2021). This has reinforced the use of their PIDs in the scientific community, and has

been the foundation for disambiguation and interlinking of institutional and biographical

data, article metadata and datasets.

Taxonomy is ruled by nomenclatural codes which state the requirements for a

nomenclatural act to be validly published, whether in print or online. These rules have

evolved with the emergence of online journals, and mandate the use of certain identifiers

within the publication and especially in the full-text XML of articles, for example the LSID of

the publication in which a new nomenclature act is published, or the mention of the ISSN

for the journal (see Penev et al. (2016) and Bénichou et al. (2018)). Hence, as a

consequence of this main mandate, we outline the use of structured data and their

identifiers to allow machines to assess whether a new taxonomic name is available

according to the Codes.

The objective of this paper is to list the main structural elements and data types present in

taxonomic publications, the existing identifiers currently in use, and make proposals for use

of additional PIDs where these do not exist yet. The paper aims at providing both

recommendations, best practices and practical advice to technical editors and publishers in

taxonomy on how to implement identifiers in their work and how they can be leveraged. For

each element, the use of an identifier is discussed from the perspective of taxonomic

publishing, its pros and cons are given, and short explanations of how and where to

implement these PIDs. We recommend that authors and publishers provide as many

identifiers and links as possible, facilitating in this way the conversion of the published

content into a digitally accessible knowledge. This would be not only a starting point for the

reuse of this important data at scale, but also spur new research based on this incredibly

rich resource. It will also allow linking data in taxonomy with other scientific disciplines to

build the future practice of evidence-based knowledge, that is to bridge the gap from a

taxonomic name to machine actionable data about it.

Publications, publication sections, sub-article data elements and

their identifiers

Modern taxonomic articles follow a rather strict structure that facilitates their representation

in a structured XML format following the widely used TaxPub* schema and enabling

efficient data exchange (Catapano 2010, Penev et al. 2012). Based on the Journal Article

Tag Set (JATS) standard* , a journal article is composed of up to three optional parts,

which should appear in the following order: Front matter is required while body and back

are optional all in that order.

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 7

In its broader sense, publishing is the act of making content available to the public. In this

paper, we refer specifically to peer-reviewed publications, either in the form of monographs

(books) or periodicals (journals), print or electronic. While not all taxonomic publications

are peer-reviewed, most of the comments and recommendations made here would apply

to them too. Publishing taxonomic content, and specifically publishing nomenclatural acts,

has a specific meaning and requires compliance to the rules, which are defined in various

codes of nomenclature.

For Zoology, the International Code for Zoological Nomenclature (ICZN)* defines a

publication in Article 8 and in its Glossary:

publication, n.

1. Any published work.

2. The issuing of a work conforming to Articles 8 and 9.

electronic publication

A publication issued and distributed by means of electronic signals.

publish, v.

1. To issue any publication.

2. To issue a work that conforms to Article 8 and is not excluded by the

provisions of Article 9.

3. To make public in a work, conforming to (2) above, any names or

nomenclatural acts or information affecting nomenclature.

In botany and mycology, the International Code of Nomenclature for algae, fungi, and

plants (ICN)* defines a publication in its Article 29:

Publication is effected, under this Code, by distribution of printed matter (through sale,

exchange, or gift) to the general public or at least to scientific institutions with generally

accessible libraries. Publication is also effected by distribution on or after 1 January 2012

of electronic material in Portable Document Format (PDF; see also Art. 29.3 and Rec. 29A.

1) in an online publication with an International Standard Serial Number (ISSN) or an

International Standard Book Number (ISBN).

Front matter of the publication

Definition

The article’s front matter contains metadata for the article and its host journal: title, authors’

list with their affiliation, the date of publication, abstracts, keywords, a copyright statement,

etc. (see front matter structures in JATS XML here* ). These front matter components

should be encoded with JATS XML elements, the following with PIDs included: the article

8Agosti D et al

itself, the journal in which it is published, and the authors (see the section on Person

names below).

Persistent unique identifiers for the front matter

International Standard Serial Number (ISSN)

Definition

The ISSN is an 8-digit number used to uniquely identify a serial publication. The system

was designed in 1971, then published as a standard in 1975, and can be used for a journal

as well as for book series, and even for some websites in the scholarly domain. It is unique

and designates the publication medium, for instance if a journal is published in both print

and digitally it must have a different ISSN for each media: a Print-ISSN and an E-ISSN (a

different ISSN should also be given for any mobile version or CD-Rom version). One also

needs an ISSN in case of a different language version of the same journal. When the

publication is provided in different media, it is recommended to display all ISSN numbers

on each version of the publication, if the latter is published, e.g. in different languages in

different journals. The ISSN does not offer any resolution mechanism and is only a media-

oriented identification.

Why does a journal need an ISSN?

The ISSN is mandatory for any journal or serial publication. In taxonomy, to be compliant

with most nomenclatural codes, the nomenclatural acts should be published in a journal or

series identified with an ISSN or a book with an ISBN.

Indeed, the International Code of Nomenclature for algae, fungi, and plants (ICN) stipulates

that a nomenclatural novelty to be considered effectively published, it should be present in

a publication distributed either in print (through sale, exchange, or gift) to the general public

or at least to scientific institutions with generally accessible libraries, or (after 1 January

2012) in an online publication with an International Standard Serial Number (ISSN) or an

International Standard Book Number (ISBN) and in Portable Document Format (PDF) (see

also Art. 29.3 and Rec. 29A.1).

The International Code of Zoological Nomenclature (ICZN) stipulates in Art. 8.5 (Ride et al.

2012) that for an e-publication to be considered published in the terms of the Code, a work

issued and distributed electronically must:

• have been issued after 2011

• have the date of publication stated in the work itself

• be registered in Zoobank (see below)

• contain the evidence of such registration (LSID of the publication or of the new

name must be indicated in the work itself).

In Zoobank, the entry must have the name of an organisation other than the publisher that

intends to permanently archive the work in a manner that preserves the content and layout,

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 9

and is capable of doing so. The ISSN or ISBN of the publication must be registered in the

Zoobank entry.

How to discover an existing ISSN

To find the ISSN of a series or journals, one may consult the ISSN portal, which provides a

comprehensive list of ISSNs and some associated metadata.

How to obtain an ISSN

To get an ISSN for a journal or series, all the necessary information, is available at https://

portal.issn.org/requesting-issn. In some countries the ISSN might not be free and may

require a registration fee between 25 € and 50 €, depending on the country assigning the

ISSN.

It seems possible to obtain an ISSN before the first publication of a print serial, however, it

is very common to be asked to wait until number 2 of the series to be printed. Online

publications are usually assigned an ISSN after the first or second issue is published (with

at least 5 publications published), or in some countries, after the website of the new

periodical has gone live and is fully functional.

How to annotate and display an ISSN

Display: ISSN: 1313-2989 (for the print version of a serial, if exists)

e-ISSN: 1313-2970 (for the online version of a serial, if exists)

For linked data purposes, it is even better to use the resolvable version of the ISSN: https://

portal.issn.org/resource/ISSN/1313-2989

Annotate in JATS:

Tag the ISSN number using the <issn> element, using the publication-format attribute to

specify the format or medium of the publication (e.g., “print”, “electronic”, “video”, “audio”,

“ebook”, and “online-only”)*

<issn publication-format="ppub">[ISSN number]</issn>

<issn publication-format="epub">[ISSN number]</issn>

Example of an ISSN

2118-9773 is the ISSN of the European Journal of Taxonomy (EJT). As the journal is an e-

only journal, it has only one online or e-ISSN.

ZooKeys has two ISSN depending on its version: 1313-2989 (for the print version)

1313-2970 (for the online version).

An ISSN can also identify a series of books, e.g. The Mémoires du Muséum national

d’histoire naturelle have one for the print version (ISSN: 1243-4442) and one for the online

version (e-ISSN: 1768-305X).

10 Agosti D et al

Sample annotation in JATS (for ZooKeys):

<journal-meta>

</journal-meta>

Recommendation

Considering that ISSN (or ISBN) are mandatory for online publication in taxonomy to be

compliant to both ICN and ICZN codes, and that an ISSN makes your journals or series

more easily identifiable and findable, attributions of an ISSN or ISBN to taxonomic

publications must be considered mandatory. A unique ISSN should be assigned to each

version of the journal, print and electronic. Each linguistic version of the journal should also

have its own ISSN.

International Standard Book Number (ISBN)

Definition

The ISBN was internationally approved as an ISO standard in 1970, and published in

1972, and is a unique international identifier for monographic publications. Correct use of

the ISBN allows different product forms and editions of a book, whether printed or digital, to

be clearly differentiated, ensuring that it identifies the specific version it relates to. Similarly

to the ISSN, each version of the book, print, e-book, pdf etc., must have a different ISBN. A

book included in a book series, or published as a monograph in a journal, can be provided

with both an ISBN and the ISSN of the series in which it is published.

ISBN is a 13-digit number that identifies a book. As it is typically used in a barcode format,

it is prefixed by an European Article Number (EAN). It is constructed as it shown in Fig. 2a.

Why does a book need an ISBN?

ISBN is important for cataloguing a book and for its findability, discovery, and

dissemination. Its display is obligatory in the first pages of the book, along with the book

title, author(s) name(s) and the publisher. ISBN is the main international record of your

publication and is important for indexing and dissemination. It aims at facilitating the

compilation of book trade directories and bibliographic databases, which in turn facilitate

their dissemination as book dealers can use them to order books efficiently and

unambiguously.

In taxonomy, it is crucial to have ISBN assigned to any taxonomic monograph with

nomenclatural acts. For instance, as explained above, Zoobank requires an ISBN to

also mentioned in the ICN Art. 29.3 as an alternative to ISSN when the nomenclatural

novelty is published in an electronic book.

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 11

How to discover an existing ISBN

As a unique identifier, ISBN is part of the metadata associated with any book. To find the

ISBN of any published book, whatever version of the book, PDF, e-book or print version, a

simple query on the internet with the title followed by the mention of the ISBN will bring the

answer. WorldCat is a good place to retrieve all the ISBNs of a book. Beware that a book

may have as many ISBNs as format versions: one ISBN for the print version, another one

for the ebook, or for second edition and so on.

How to obtain an ISBN

All the information needed to get an ISBN for a publication is available at https://www.isbn-

international.org/content/how-get-isbn.

When an ISBN has been assigned to a publication, it should always be displayed to

facilitate its identification. The ISBN is also crucial for dissemination as it is displayed in a

barcode format, so libraries and bookshops can process incoming stock and outgoing

sales quickly and accurately. On a printed book, an ISBN should be included on the

room on the copyright page. If there is no barcode, then the ISBN should also be on the

back cover or jacket preferably on the lower right. Each version of the book needs to be

provided with its own ISBN. More details on when to assign an ISBN are available at https:/

/www.isbn-international.org/content/isbn-assignment.

The publisher will then fill in the ISBN in the legal deposit form with all the additional

metadata of the book for cataloguing purposes at their respective national ISBN agencies.

How to annotate and display an ISBN

Display: ISBN: 978-2-85653-939-2

Annotate in JATS:

Figure 2.

Construction pattern of

a: ISBN

b: DOI

12 Agosti D et al

Tag the ISBN number using the <isbn> element, using the publication-format attribute to

specify the format or medium of the publication (e.g., “print”, “electronic”, “video”, “audio”,

“ebook”, and “online-only”)*

<isbn publication-format="[format type]">[ISBN number]</isbn>

Example of an ISBN

The Flora of New Caledonia published by the Muséum national d’Histoire naturelle in 2020

on Apocynaceae, Phellinaceae and Capparaceae has an ISBN for its print version

(978-2-85653-939-2), one for the PDF version on sale (978-285653-954-5) and one for its

bundle (print + e-book: 978-2-38036-955-2).

Sample annotation in JATS with multiple ISBN numbers:

<book-meta>

<book-meta>

Recommendation

An ISBN is mandatory to properly identify a published book. Each version of the book

(PDF, print, ebook, each linguistic version, second edition) should have its own ISBN.

Considering that ISSN and ISBN are mandatory for nomenclature purposes, we must

consider the use of ISBN mandatory for taxonomic publications.

Digital Object Identifier (DOI)

Definition

The DOI system has been developed by the DOI Foundation and is implemented through a

federation of registration agencies. The two most commonly used agencies that register

DOIs in the scholarly domain are Crossref and DataCite. Both are membership

organisations providing DOIs to research outputs but for different purposes. The main

difference lies in the type of digital objects they identify, the scale of numbers of DOIs

needed and the metadata associated with the DOI.

Crossref is a non-profit membership organisation specifically serving scholarly publications.

Its members are publishers, research institutions, university presses, societies and

funders. Membership in Crossref is open to organisations that produce professional and

scholarly materials and content. In addition, applicants should be able to meet the terms

and conditions of membership.

DataCite is a global non-profit organisation that provides persistent identifiers (DOIs

specifically) for research data and other research outputs and resources. DataCite’s

members work with data centres, stewards, libraries, archives, universities, publishers and

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 13

research institutes that host repositories and who have responsibility for managing,

holding, curating, and archiving data and other research outputs.

In their respective websites, a schema (Fig. 3) explains the rationale behind each of these

two agencies (e.g. https://www.crossref.org/community/datacite/).

The DOI includes three parts Fig. 2b:

To create the DOI, the DOI prefix given to an organisation is combined with a suffix of

choice. The DOI becomes active once registered with a DOI registration agency like

CrossRef or DataCite. CrossRef provides a complete documentation on best practices to

construct the suffixes.

Figure 3.

Dichotomic decision tree for the registration of CrossRef and DataCite DOIs, from the

DataCite - Crossref release.

14 Agosti D et al

How to discover an existing Digital Object Identifier (DOI)?

To find the corresponding DOI registered, enter the title, the author or any metadata in

Crossref or DataCite search engines or use alternatively the ReFindit tool.

How to mint a Digital Object Identifier (DOI)

All agencies providing DOIs are listed here: https://www.doi.org/registration_agencies.html.

Each of them may have different rules and apply different fees. Alternative repositories to

mint DOI for legacy publications are the Biodiversity Heritage Library, the Biodiversity

Literature Repository and institutional libraries retro-digitising legacy publications, such as

E-Periodica at the Federal Institute of Technology, Zurich.

To deposit a DOI to Crossref,one has to be a member. Membership fees begin at 275 USD

and depend on the revenue of the applicant. Once a member, a DOI prefix is assigned to

the joining organisation and will form the stem of links to all its metadata records. Fees

vary per record type, books, research grants, preprints, etc., from 0.15 USD for a legacy

article to 1 USD for a newly published article. Each DOI has to be registered by direct

deposit of XML, using Open Journal System Plugin for instance or, alternatively, through an

online web deposit form.

Component DOIs are often registered for figures, tables, and supplemental materials

associated with a journal article. They have their own metadata distinct from that of the

parent article DOI.

The registration of the DOI includes all the metadata, i.e. basic information such as dates

of publication, publication outlet, including the ISSN or ISBN, article title and authors. There

is a Crossref membership obligation: accurate metadata should be deposited for all DOI

registered, and the metadata should be maintained for the long term, including updating

any URLs that change. It is also an obligation to include DOIs in the reference lists for

existing works which have DOIs. A free public API is available to retrieve all existing

Crossref DOIs.

To register a DOI with DataCite, one has to be a member. Membership is open to all

organisations whose missions include research output sharing. A membership fee of 2,000

euros applies to member organisations. Once a member, non-for-profit members will have

to pay another 500 € annual fee to make use of DOI registration services. Each DOI, up to

1,999, will cost 0,80 €. There are two ways to register a DOI: using an API or a Web

Interface. All information is provided at https://support.datacite.org/docs/getting-started.

How to annotate and cite a DOI

Cite:

https://doi.org/10.3897/zookeys.1083.72939 (preferred), or DOI: 10.3897/zookeys.

1083.72939

Annotate in JATS:

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 15

Tag the cited DOI with the <ext-link> element, using the xlink-href to provide the DOIs https

version and the ext-link-type attribute with value “doi”.*

<ext-link xlink:href="[https-version of DOI]" ext-link-type="doi">

[https-version of DOI]

</ext-link>

Example of a DOI

https://doi.org/10.3897/zookeys.1083.72939 refers to an article published in ZooKeys.

Sample annotation in JATS:

<ext-link xlink:href="https://10.3897/zookeys.1083.72939" ext-link-type="doi">

https://doi.org/10.3897/zookeys.1083.72939

</ext-link>

Recommendation

Use Crossref DOI for articles and bibliographic references. For supplementary material,

figures or tables, create Crossref component DOI or DataCite DOI. Generate a DataCite

DOI for data. If none is available, try to find a way to create a DOI using an alternative

repository such as BHL, BLR or E-Periodica, or DOIs issued for datasets deposited at

large international repositories, such as GBIF, DataONE, Dryad, Zenodo and others.

Display all the identifiers, ISSN, ISBN, DOI, on the corresponding publication page and

DataCite. Always include the DOI in the metadata for other publication-related registration

purposes, for example at ZooBank, IPNI, MycoBank, Zenodo, Dryad and others.

Body of the article

Definition

Most academic journals require the authors to write their articles following the IMRaD

format. IMRaD stands for Introduction, Method, Result and Discussion which are the four

main sections that constitute the structure of most scientific papers in the Science,

Technical and Medical (STM) fields. The body of the article is the main textual and graphic

content of the article and is situated between the front and the back matters. This usually

consists of sections, subsections, and paragraphs, which may themselves contain figures,

tables, etc.

In a taxonomic article, the body of the article includes specific items, such as taxonomic

treatments, material citations, descriptions, differential diagnoses, details of collecting

permits, etc.

16 Agosti D et al

Sections

Definition

Most journal articles are divided into sections, each with a title that describes the content of

the section, such as “Introduction”, “Materials and Methods”, or “Conclusions”* . A special

section in taxonomic publications is the taxonomic treatment as described below. The

different sections include different kinds of data and information that are important to

reproduce the research. For example, the section “Materials and Methods” lists the

collections studied, software used to analyse the data, or instruments used to make

measurements.

What are the identifiers for sections

Sections are normally tagged with internal Universally Unique Identifiers UUIDs in the

article XML. In addition, the names of the sections, which are used more or less

consistently in various science domains, e.g., “Introduction”, “Material and Methods”,

“Results”, “Conclusions” etc. can be used for inferring a semantic meaning of their content,

an approach that is currently used for the conversion to RDF and export to the OpenBioDiv

knowledge graph.

How to annotate sections

In JATS, the sections are annotated using the following elements and attributes:

<sec-meta>

<mixed-citation>

</mixed-citation>

...

</sec>

The sec-type attribute annotates the basic structural unit of the body of a document.

Following the recommendation that sec-type “is most useful when a list of values is

maintained, and articles are tagged accordingly”, for JATS the values: "cases",

"conclusions", "discussion", "intro", "materials", "methods", "results", "subjects",

"supplementary-material", are recommended.*

The “id” attribute is a unique internal identifier of an element; it allows the element to be

cross-referenced [and linked to]. The value must be unique across a document…[id] holds

an internal document identifier that can be used by software to perform a simple link. An id

should not be confused with elements that are used to hold externally defined identifiers

such as a DOI”* . For an externally defined identifier assigned to the section, a <sec-

meta>* element may be used to provide metadata for a section, which includes <mixed-

citation>* containing an <object-id>* element to record an identifier, for example, a

UUID.

16 17

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 17

Though not recommended, a lighter-weight solution for associating an external identifier

with a section is to “overload” the id attribute of <sec> by using an external identifier such

as a UUID as the value. However, the “id” attribute “must start with a letter of the alphabet”*

, so UUIDs (which may start with a digit) should be prefixed with a string starting with an

alphabetic character, e.g., “uuid-”, to validate.

Example

Annotation of a section “Methods” including an object identifier taken from the article of

Bueno-Soria et al. (2022).

<sec-meta>

<mixed-citation>

object-id>

</mixed-citation>

</sec-meta>

<title>Methods</title>

<p>The specimens of the genus <em>Xiphocentron</em> studied here were borrowed

from the collections of the National Museum of Natural History, Smithsonian Institution in

Washington, DC, and from the Colección Nacional de Insectos, Instituto de Biología de la

Universidad Nacional Autónoma de México.</p>

<p>The type materials are deposited as indicated in each species description,

in the collections: National Museum of Natural History, Smithsonian</p>

</sec>

Recommendation

Section and subsection titles should be tagged as such and Internal UUIDs should be

assigned to them in the article XMLs.

Figures, figure captions and citations

Definition

A figure is either a photo or a scientific drawing illustrating biological species or part(s) of

them, landscapes, habitats or equipment, or visualisation of data or results from statistical

analyses. Figures and their captions convey an essential part of the information contained

in a scientific paper and are of particular interest for the community.

The ICN states the importance of illustrations in its Art. 43.2:

“A name of a new fossil-genus or lower-ranked fossil-taxon published on or after 1 January

1912 is not validly published unless it is accompanied by an illustration or figure showing

the essential characters or by a reference to a previously and effectively published such

illustration or figure.”

According to article 40.3, illustrations can also be a type specimen prior to 1 January 2007*

18 Agosti D et al

The figures related to a taxonomic treatment (see definition below) are usually cited at the

beginning of the treatment and are part of it.

What are the identifiers for figures

DOIs being either Crossref component DOIs or DataCite DOIs are usually used when the

figures are deposited in a repository.

How to mint an identifier for a figure

For minting DOIs, see section “Digital Object Identifiers” above. If no DOIs are minted for

figures, these can be identified with internal UUIDs minted by software during the

compilation of the full-text article XML, and a hash of the figure allows to uniquely identify

the respective figure.

How to annotate and cite a figure, figure caption and figure citation

Cite: Figures are cited within the text following the long-established practice in scholarly

publishing (e.g., “according to Fig. X” or “see detail (Fig. Y)”). Citation style should follow

the journal’s or publisher’s instructions for the authors.

Annotate in JATS:

Figure:

</fig>

In-text figure citation:

[Figure reference]

</xref>

Note that the citation details of the figure as delivered by the Biodiversity Literature

Repository (BLR) at Zenodo should contain both the DOI of the article and the component

DOI of the figure. In the case where no CrossRef component DOI exists, a DataCite DOI is

minted for the figure at BLR. The “rid” (reference to an identifier) attribute is needed to

perform the linking with the <fig> element via the embedded “id” element.

Examples

Annotation of a figure and in-text figure citation (from Blahnik and Andersen (2022)):

Figure:

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 19

<p>

Malaise trap across Kaputu Stream at 1535 m altitude in the Mazumbai Forest Reserve in

the West Usambara Mountains, northeastern Tanzania (Photo: Trond Andersen).</p>

</caption>

</fig>

In-text figure citation:

https://doi.org/10.3897/zookeys.1088.78139.figure1 is a CrossRef component DOI

assigned to Figure 1 of the article https://doi.org/10.3897/zookeys.1088.78139.

Recommendation

Use Crossref component DOI to identify each figure within an article. The component DOI

has the important feature of a link from the figure DOI to its parent article DOI. If no

Crossref DOI is available, use alternatives from DataCite.

In all cases, and especially if no DOIs are minted for figures, it is recommended to assign

internal UUIDs minted by software during the compilation of the full-text article XML as well

as a hash for unique identification.

When compiling the full-text XML, it is highly recommended to cross-reference (anchor) the

in-text figure citations to their respective figures in the article body.

Tables, table citations

Definition

A table is a concise and effective way of presenting large amounts of data usually

displayed in rows and columns for reference.

Tables are increasingly important because they contain, in many cases, a compilation of

the specimens used, their sequence accession codes, specimen codes that allow linking to

the cited specimens, as well as traits, such as measurements or qualitative descriptions or

even the results of an analysis performed on the raw data taken from the specimens or

from their environment. Each row can be envisioned to represent a structured material

citation, and if used to list species used in a study, together with a taxonomic name, an

entire taxonomic treatment.

What are the identifiers for table

In TreatmentBank, tables are identified by a UUID and a persistent http URI ID. In the

Pensoft article XMLs, tables are identified by internal UUIDs.

20 Agosti D et al

How to mint a table identifier

DOIs or Crossref component DOIs relating to the article, should be minted and submitted

for registration to Crossref by the publisher. If no DOIs are minted for tables, these can be

identified with internal UUIDs minted by a software during the compilation of the full-text

article XML.

Annotating and citing tables

Tables are cited within the text following the long-established practice in scholarly

publishing (e.g., “according to Tab. X” or “see data (Tab. Y)”). Citation style should follow

the journal’s or publisher’s instructions for the authors.

Annotate in JATS:

Table:

<table-wrap id="[Internal identifier]">

<table>

...

</table>

</table-wrap>

In-text table citation:

<xref ref-type="table" rid="[Internal identifier]">[Table reference]</xref>

The “rid” attribute is needed to perform the linking to the <table> element via the “id”

attribute of the target <table-wrap> element, which itself has optional, repeatable <object-

id> elements recording identifiers for the table it contains. The JATS tag library defines the

an article (for example, for a figure or a table)”, further stating that, “the <object-id> element

holds an external identifier, typically assigned to an object such as a table by a publisher.

The contents of this element should not be confused with the "@id" attribute, which holds

an internal document identifier that can be used by software to perform a simple link inside

the document.”*

Examples

Annotation of a table and in-text table citation (from Blahnik and Andersen (2022))

Table:

<table-wrap id="T1">

10.3897/zookeys.1111.77586.table1

</object-id>

<caption>Table 1. African genus Chimarra</caption>

<table>

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 21

...

</table>

</table-wrap>

In-text citations:

Recommendation

Ideally, a table should be provided with a Crossref component DOI related to the article. In

all cases, and especially if no DOIs are minted for tables, it is recommended to assign

internal UUIDs minted by software during the compilation of the full-text article XML.

When compiling the full-text XML, it is highly recommended to cross-reference (anchor) the

in-text table citations to their respective tables in the article body.

Taxonomic treatments

Definition

Taxonomic treatments are sections of publications documenting the features or distribution

of a related group of organisms (taxon) (Catapano 2010). Each taxonomic name relates to

at least one taxonomic treatment: a publication, or more frequently a section of a

publication documenting the features of a taxon in ways adhering to highly formalised

conventions. Some of these descriptions are over two centuries old and are maintained by

taxonomic community ethical and professional norms regulated by the Nomenclatural

Codes. The modelling of taxonomic treatments in TaxPub XML is designed to follow the

FAIR principles and provide clarity and repeatability of the research, which both are integral

parts of the modern evidence-based science.

The features and structure of treatments have changed over time, and vary between and

within publications. Often an indication follows the name of whether the taxon is new to

science, e.g., “species nova”, “sp. nov.” or “genus novum”, “gen. nov.” and the name or

names of the persons who attribute the naming. A listing of taxa that are already known to

science, citations of earlier treatments (treatment citations), often follows in a section. In

cases when taxonomic names change as a result of a taxonomic revision, for example

because of a raise in its rank, or because a taxon is synonymized, this is followed by a

label stating the change, such as for example “syn. nov.” or “nov. stat.”. Other information,

such as persistent identifiers and references to physical specimens, may also be included

in a treatment.

A number of other sections may follow the nomenclature section. One of the most

significant sections, frequently titled “Materials Examined”, includes citations to specimens

used as the basis of the treatment and data about their properties (e.g., DNA sequences).

This section often includes the circumstances of collection and/or deposition at a museum

or other institution. Historically, these details have allowed scientists to visit the holding

22 Agosti D et al

institution, or to seek a loan, for further scientific investigation of the same material

that

was described by the treatment. Also common is a “Description” section providing

information — often in highly structured language, and sometimes in tabular form — on the

distinctive features of the collected organisms, with an aim toward characterising the entire

taxonomic class such material represents.

Similar to a “Description” section, there is a “Diagnosis” section, which contains

descriptions of only those features or unique combinations of features “that distinguish that

species from others, in the same way that the disease identification you receive when you

visit the doctor is called the diagnosis because the doctor has distinguished your illness

from all other possibilities based on the basis of your symptoms and tests” (Winston 1999).

Most treatments describing new taxa include an “Etymology” section explaining the origin

of the assigned Latin name, a “Distribution” section summarising the spatial and temporal

distribution of the taxon, or an “Ecology” section discussing behaviour and relationships to

habitat or details on the environmental variables measured during the collecting events of

the specimens. For higher level taxa (such as genera and families) a “Key” presenting a

set of instructions, in the form of a decision tree or even workflow, for distinguishing lower

level taxa from one another is also common (Catapano 2010).

Similar to publications and following the FAIR principles, the treatments can be extracted

from the publications, preserved separately and made freely accessible to the public

(Fig. 4; Agosti and Egloff 2009, Patterson et al. 2014).

An XML tagset for Taxonomic treatments has been formalised as an extension of the

Journal Article Tag Suite (JATS) (Catapano 2010), and adopted in 2010 by Pensoft

Publishers in their journal production process (Penev et al. 2010), now including 38

journals* . The export of treatments from published PDFs has been adopted by CETAF’s

European Journal of Taxonomy and Muséum national d’Histoire naturelle (5 journals* ).

Legacy publications are annotated and treatments are made accessible by TreatmentBank

(780,000 treatments as of August 2022) and the Biodiversity Literature Repository

(390,000 treatments), including current content from 52,000 articles. Together with the

treatments exported by Pensoft, the total number of processed articles exceeds 70,000.

Treatments are reused by GBIF upon extraction, where they are imported as part of a

dataset in a Darwin Core Archive format compiled from taxonomic treatments and cited

figures. Currently these article-based datasets represent almost 60% of all the datasets

published in GBIF.

In Wikidata, taxonomic treatments can be annotated with the property taxonomic treatment

(P10594)* , with protologue as a subclass referring to the treatment used to describe a

new taxon, that is to create an available name sensu the ICN.

The Barcode of Life Data Systems (BOLD) Barcode Identification Numbers (BINs)

(Ratnasingham and Hebert 2013) are functionally similar to treatments, though they are not

sections of taxonomic publications and provide less information. BINs are dynamically

generated by the Barcode of Life Data System (BOLD), through an online framework that

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 23

clusters barcode sequences and generates an identifier and web page for each cluster.

This framework uses a clustering algorithm based on graph theoretic methods to assign

BINs (Ratnasingham and Hebert 2013). Each BIN is assigned two identifiers, a resolvable

URI generated by BOLD, that consists of an alphanumeric identifier composed by the

prefix BOLD followed by 3 letters and a 4-digit number (e.g., BOLD:AAA0111), and a DOI.

When the submission of new information leads to the merge of two BINs, the most recently

registered BIN is synonymized. But, when the analysis splits a BIN into two, new BINs are

established and a disambiguation option is suggested. In any case DOI amendments are

made to ensure that original identifiers are not lost.

The UNITE Species Hypotheses (SHs) are functionally similar to treatments including all

the clustered public fungal ITS sequences to which a unique DOI is assigned by UNITE.

UNITE is a database and sequence management environment for the molecular

identification primarily of fungi but now also of other taxa. It focuses on nuclear ribosomal

Figure 4.

An example of a treatment accessible in various formats. Source: https://

europeanjournaloftaxonomy.eu/index.php/ejt/article/view/1639/5873

Alternative format:

TreatmentBank (TB) HTML: https://tb.plazi.org/GgServer/html/03E2AB75FFD6BE60FE39

FCF5FBF9F83B

TB XML: https://tb.plazi.org/GgServer/xml/03E2AB75FFD6 BE60FE39FCF5FBF9F83B

TB RDF: https://github.com/plazi/treatments-rdf/blob/main/data/03/E2/AB/03E2AB75FFD6BE

60FE39FCF5FBF9F83B.ttl

BLR: http://doi.org/10.5281/zenodo.6302070

GBIF: https://www.gbif.org/species/193266458

24 Agosti D et al

internal transcribed spacer (ITS) region sequences that are considered the fungal barcode.

All species hypotheses have a unique URL where the associated public sequences are

displayed (Nilsson et al. 2019). These sequences are referenced through their accession

numbers and linked to their original records at International Nucleotide Sequence

Database Collaboration (INSDC, Arita et al. 2021).

What are the identifiers for taxonomic treatments

DOI

A subtype “taxonomictreatment” has been added in Zenodo as a DataCite digital object

identifier (DOI) to the “publication” type. The metadata for taxonomic treatments in Zenodo

are enhanced with added custom keywords based on existing domain specific

vocabularies (e.g., Darwin Core), links to the source publication, cited figures or related

identifiers such as the http URIs minted by TreatmentBank (see below). In case of

treatments deposited in BLR via TreatmentBank, the respective HttpURI are included in the

metadata.

For BINs* and Species Hypotheses* , DataCite DOIs are minted.

HTTP URI

The “HttpURIs” were created by Plazi for treatments in 2009 parallel to the development of

the persistent HTTP URIs for specimens now widely accepted in CETAF. The HTTP URIs

are used by GBIF when reusing TreatmentBank treatments. The HTTP URIs are kept

persistent and are built based on a unique UUID and the prefix “http://treatment.plazi.org/

id/UUID” (e.g., http://treatment.plazi.org/id/0000C505-BB5D-484C-76BE-9AB6999DEB23).

The original intention was to share the UUID with Zoobank whereby the Zoobank UUID

would resolve to the taxonomic name and to the respective taxonomic treatment in

TreatmentBank. Unfortunately this synchronisation has been discontinued.

UUID

During the publication of a taxonomic article, Pensoft journals assign UUIDs to each taxon

treatment. Those UUIDs are further used by Plazi to mint the HTTP URIs of the treatments

at TreatmentBank.

How to discover treatment identifiers

The DOI of a treatment can be found by searching ReFindit or for those minted by

Biodiversity Literature Repository, through the search engines of Zenodo or

TreatmentBank. The HTTP URIs can be found through GBIF or the Biodiversity Literature

Repository (BLR) or TreatmentBank.

Via ReFindit API (search by author, year, and taxon name, the latter as title):

24 25

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 25

https://refindit.org/find?search=advanced&author=Kronestedt&year=2011&

title=Pardosa%20zyuzini (requires some further matching to pick correct result)

Via Zenodo UI (full text search):

https://zenodo.org/search?page=1&size=20&q=Pardosa+zyuzini+Kronestedt+2011

Via TreatmentBank statistics API (exact match search on author, year, and taxon name):

https://tb.plazi.org/GgServer/srsStats/stats?

outputFields=doc.uuid+bib.author+bib.title+bib.pubDate+bib.origin+bib.firstPage+bib.lastP

age+bib.articleFirstPage+bib.articleLastPage+tax.name+tax.genusEpithet+tax.speciesEpit

het+tax.authName+tax.authYear+tax.status&groupingFields=doc.uuid+bib.author+bib.title+

bib.pubDate+bib.origin+bib.firstPage+bib.lastPage+bib.articleFirstPage+bib.articleLastPag

e+tax.name+tax.genusEpithet+tax.speciesEpithet+tax.authName+tax.authYear+tax.status

&format=JSON&FP-tax.name=%22Alloplasta%25japonica%22&FP-

tax.authName=Watanabe&FP-tax.authYear=2022 (simplified API under development)

Via TreatmentBank UI search (fuzzy search for taxon name):

https://tb.plazi.org/GgServer/search?taxonomicName.isNomenclature=true&

taxonomicName.exactMatch=true&taxonomicName.taxonomicName=Pardosa+zyuzini

Via GBIF UI (dataset search):

https://www.gbif.org/search?q=Prosymna+lisima

Via GBIF API (species search):

http://api.gbif.org/v1/species?name=Prosymna+lisima

How to mint an identifier for treatment

Currently, Zenodo is the only place to mint a DOI for a treatment. UUIDs are generated by

some publishers during the article processing before publication (all Pensoft journals, for

example). HTTPURIs are minted by TreatmentBank. This is not an exclusive solution,

however, since a treatment is a subtype of the DataCite publication type at Zenodo.

How to annotate and cite treatments

Cite: A citation of a treatment can be provided either by its DOI or its HTTP URI generated

by Plazi’s TreatmentBank. The citation of other treatments normally happens within a given

treatment’s Nomenclature section (in the so-called “nomenclature-citation-list” of the JATS/

TaxPub XML representation), where they can also introduce a nomenclatural change,

indicated with a label (e.g. syn. nov., comb. nov., nom. nov., etc.).

Annotate in JATS (treatment and subsections in JATS/TaxPub):

26 Agosti D et al

<tp:taxon-treatment>

<tp:treatment-meta>

<mixed-citation>

</mixed-citation>

</tp:treatment-meta>

</tp:taxon-treatment>

For the nomenclature subsection:

<tp:nomenclature>

<tp:taxon-name>[Taxon name]</tp:taxon-name>

</tp:nomenclature>

For all other subsections:

<tp:treatment-sec sec-type="[section type name]"> ... </tp:treatment-sec>

Section types should, if possible, make use of the following vocabulary terms: description,

diagnosis, discussion, distribution, ecology_behavior, conservation, etymology,

materials_examined, reference_group, and vernacular_names which will add a semantic

meaning to (sub-)section titles and facilitate the extraction and reuse of the data.

Examples

Annotation of treatments, nomenclature section and subsections:

Treatment:

<tp:treatment-meta>

<mixed-citation>

</mixed-citation>

Nomenclature section:

<tp:nomenclature>

<tp:taxon-name>Tribasodites yatung</tp:taxon-name>

</tp:nomenclature>

Subsection:

<tp:treatment-sec sec-type=”description"> ... </tp:treatment-sec>

Recommendation

Tag each taxonomic treatment in the article full-text XML and then assign a CrossRef

Component DOI or Datacite DOI or internal UUID for it. Register all the metadata

associated with the DOI.

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 27

Treatment citations

Definition

A treatment citation is a reference to a previous treatment, in many cases the original

description of the taxon, or protologue (Fig. 5). Treatment citations reflect the history of the

taxon and its nomenclatural relationships with other taxon concepts, either by indicating a

change proposed in the treatment, e.g. a new synonymy or a new combination, or by

reconfirming previous changes. They also refer to treatments that contributed new

research results to an existing taxon. Thus, treatment citations can be grouped in several

categories, e.g. by type of a nomenclatural change (“syn. n.”, “comb. n.”, etc.) or by

confirmation of previous taxon name status, and those categories allow formal annotation

during the text mining process and further-re-use.

Treatment citations are the source and basis for creating synonymic lists and taxonomic

catalogues.

Treatment citations are analogous to bibliographic references in a publication citing

previous works.

Figure 5.

Treatment citation. Green boxes: treatment citations. A. published example. B: annotated

treatment citations in TreatmentBank using TB internal XML.

Source: https://europeanjournaloftaxonomy.eu/index.php/ejt/article/view/787/1829

TreatmentBank XML: https://treatment.plazi.org/GgServer/xml/101687E3D558FFC3FDF9

A837FECED008

28 Agosti D et al

What are the identifiers for treatment citations

No identifiers are known, however, citations can and should be tagged in the backend XML

of the article to be made discoverable and processed for further use.

How to discover treatment citations

Treatment citations are listed subsequent to the nomenclatural sections of a taxonomic

treatment. They usually consist of a taxonomic name, the authority and year, and a page

number, especially in zoology. In combination, the authority and year are also a

bibliographic citation of the original publication of the respective treatment, albeit often

implicit, because traditionally, taxonomists do not include this kind of bibliographic

references in the article reference list (Bénichou et al. 2018). This procedure has now been

suggested by CETAF, BHL and SPNHC (Benichou et al. 2022) and is strongly encouraged

by Pensoft’s journals. In case of multiple citations for the same taxonomic name, a further

element (treatment citation list) is included that allows that the taxonomic name does not

need to be repeated in each case.

How to mint an identifier for treatment citation

There is no established procedure for minting treatment citations, except for possible

assignment of internal UUIDs to them.

How to annotate and cite a treatment citation

The treatment citation annotations are attributed with persistent HTTP URIs of the

respective treatment(s) in TreatmentBank. The treatment citation element is currently being

remodelled and thus the recommendations might change in the next version of TaxPub.

Annotate in JATS/TaxPub:

<tp:nomenclature>

<tp:taxon-name>

<tp:taxon-name-part taxon-name-part-type="genus">Cus</tp:taxon-name-part>

<tp:taxon-name-part taxon-name-part-type="species">dus</tp:taxon-name-part>

</tp:taxon-name>

<tp:nomenclature-citation-list>

<tp:nomenclature-citation>

<tp:taxon-name>Aus bus</tp:taxon-name>

<mixed-citation>

[DOI]

</object-id>

</mixed-citation>

</tp:nomenclature-citation>

</tp:nomenclature-citation-list>

</tp:nomenclature>

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 29

Example

Annotation of treatment citation in the treatment of Chondrocyclus convexiusculus (Pfeiffer,

1855) in Cole (2019):

<tp:nomenclature-citation-list>

<tp:nomenclature-citation>

<tp:taxon-name>Cyclostoma (Cyclophorus) convexiusculum</tp:taxon-name>

Pfeiffer, 1855: 104

(Type loc.: Simonstown [Macgillivray]).

</tp:nomenclature-citation>

<tp:nomenclature-citation>

<tp:taxon-name>Cyclophorus convexiusculus var. minor</tp:taxon-name>

Benson, 1856: 438

(type loc.: Table Mountain [Layard]).

</tp:nomenclature-citation>

</tp:nomenclature-citation-list>

<tp:nomenclature-citation-list>

<tp:taxon-name>Chondrocyclus convexiusculus</tp:taxon-name> –

<tp:nomenclature-citation>Kobelt 1902: 230</tp:nomenclature-citation>

<tp:nomenclature-citation>Connolly 1939:536</tp:nomenclature-citation>

<tp:nomenclature-citation>Herbert & Kilburn 2004: 92</tp:nomenclature-citation>

</tp:nomenclature-citation-list>

Recommendation

Treatments should be cited by their PIDs, either through their inclusion in a nomenclature-

citation in a nomenclature section of the citing treatment or as a standalone in-text citation

in any part of the article as follows: “Based on Treatment: [hyperlinked treatment PID,

where a treatment PID can be either the DOI of the treatment provided by BLR or Plazi’s

HTTP identifier available from TreatmentBank] I conclude that ....”.

Treatment citations should be tagged in the article XML as separate entities and, if

available, should contain the existing PIDs of the cited treatments.

Recently, a joint statement of CETAF, SPNHC and BHL has been published (Benichou et

al. 2022) recommending extended citation details of taxon names by adding richer

bibliographic citation detail to each taxon concept. We provide here a shortened version of

these recommendations:

1. Provide each scientific name of a taxon, at least on its first mention in the paper,

with authorship, date, and corresponding entries to the publication’s “Bibliographic

references” section.

2. If the publisher’s guidelines do not allow you to list it as a reference, cite it properly

as a bibliographic reference by adding the page number after the date for instance.

For example, for a species described in EJT http://dx.doi.org/10.5852/ejt.

2022.828.1851 on p. 48, it is preferable to use the notation Infrantenna fissilis Liu &

Sittichaya, 2022: 48 instead of Infrantenna fissilis Liu & Sittichaya, 2022.

30 Agosti D et al

3. Provide the corresponding persistent identifier (PID) to each of these references

where they exist, i.e. a Crossref DOI minted by the publisher or minted by the

Biodiversity Heritage Library (BHL) when the legacy publication has been digitised

retrospectively and provided with a DOI, or a DataCite DOI minted by organisations

digitising legacy literature (e.g., e-Periodica at the Federal Institute of

Technology

Zurich) or the Biodiversity Literature Repository (BLR) at Zenodo.

4. Provide the PID of the taxonomic treatment where they exist, using for instance, the

DOI of the treatment deposited in BLR, or for articles with primary taxonomic

descriptions minted by BHL (for example: https://www.biodiversitylibrary.org/part/

304567).

Material citations

Definition

A material citation is a reference to, or citation of, one or multiple specimens in scholarly

publications (https://dwc.tdwg.org/terms/#materialcitation; Chester et al. 2019). Material

citations can be situated within the respective treatments, in tables, or as supplementary

material, and refer to the specimen data used in the study. They provide the best, expert-

curated identification of specimens in collections including, in many cases, explicit links to

the institution, specimen, gene sequences and geographic data. Often they are the only

evidence of the existence of a specimen in the digital world, for example, if published

through the GBIF infrastructure.

The GBIF occurrences can create a rich linking network for specimens because a GBIF

specimen record can be linked to a material citation published in a scholarly article, or at

least to the treatment or publication containing that record.

What are the identifiers for material citations

TreatmentBank and the Biodiversity Data Journal issue internal UUIDs for material

citations. They are reused in conjunction with the treatment UUID in GBIF in the form of

“treatment UUID.mc.material citations UUID”. GBIF is minting an identifier for each material

citation present as an occurrence record in their infrastructure. TB maintains the links and

identifiers of the occurrences in GBIF with their respective material citations in

TreatmentBank.

How to discover material citations' identifiers

These identifiers are currently minted post-publication by TreatmentBank, or before

publication by the Biodiversity Data Journal, and can be found using TreatmentBank data

access interface (https://tb.plazi.org/GgServer/srsStats) which can also provide access to

the related GBIF occurrence ID.

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 31

Via TreatmentBank statistics UI with a wide variety of search fields and output fields to

choose from. The link (visit TreatmentBank statistics UI) shows taxon name, author, year,

and type status.

Via TreatmentBank statistics API with a wide variety of search fields and output fields to

choose from in the UI. The link (visit TreatmentBank statistics API) shows taxon name,

author, year, and type status, retrieved as JSON. A more simplified API is under

development.

Via GBIF API (occurrence search for taxon name, restricted to materials citations).

http://api.gbif.org/v1/occurrence/search?

basisOfRecord=MATERIAL_CITATION&scientificName=Lebertia+insignis Other search

fields are also available, e.g. country, might require further matching efforts to find

additional matches from specific source publications in GBIF.

How to mint an identifier for material citation

Follow your standard procedure for minting UUIDs.

How to annotate and cite material citation

Annotate in JATS/TaxPub:

Use “object-id” to provide an identifier for a material citation in the article which allows it to

be cited unambiguously.

<tp:material-citation>

[material citation string]

</tp:material-citation>

To provide an external identifier for a component of a material citation (e.g., a catalog

number or occurrence id), use <named-content>, specifying the type of identifier in the

content-type attribute.

<named-content content-type="[content type]">[Identifier]</named-content>

The <uri> element may be used to tag an identifier that is a URI and provide a live link to

the representation of the identified resource:

<named-content content-type="[content type]">

</named-content>

Examples

A material citation from Monomorium dryhimi that can be unambiguously cited (Sharaf and

Aldawood 2011).

32 Agosti D et al

<tp:material-citation>

Holotype worker. SAUDI ARABIA, Al Bahah province, Amadan forest, Al Mandaq

governorate, 20°12'N, 41°13'E, 1881 m.a.s.l. 19.V.2010 (M. R. Sharaf &

A. S. Aldawood Leg. KSMA

</tp:material-citation>

A material citation citing a specimen from the MNHN Paris (Paton et al. 2016)

<tp:material-citation>

<named-content content-type="dwc:occurrenceID">

http://coldb.mnhn.fr/catalognumber/mnhn/p/p04158076

</uri>

</named-content>

…

</tp:material-citation>

Finer grained markup

<tp:material-citation>

<tp:type-status>Holotype</tp:type-status> worker.

<tp:material-location>King Saud Museum of Arthropods (KSMA),

College of Food and Agriculture Sciences, King Saud University, Riyadh,

Kingdom of Saudi Arabia.

</tp:material-location>

<tp:collecting-event>

<tp:collecting-location>

<tp:location>

SAUDI ARABIA, Al Bahah province, Amadan forest, Al Mandaq governorate

</tp:location>

</tp:collecting-location>,

<named-content content-type="dwc:verbatimCoordinates">

20°12'N, 41°13'E

</named-content>, 1881 m.a.s.l. 19.V.2010 (

<named-content content-type="dwc:recordedBy">

M. R. Sharaf

</named-content> &

<named-content content-type="dwc:recordedBy">

A. S. Aldawood

</named-content> Leg.);

</tp:collecting-event>

</tp:material-citation>

Besides GBIF issuing an occurrence ID for the material citations, and Pensoft’s

Biodiversity Data Journal, no other publishers are using IDs for material citation so far. For

EJT and the journals of the MNHN Paris, Plazi is adding the material citations attribute

after extracting the data from the published papers.

In legacy publication annotations, material citations are attributed with a unique UUID in

TreatmentBank. These UUIDs are resolvable via Plazi SRS* , and are included in the

Darwin Core Archive submitted by TreatmentBank to GBIF where they are reused in

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 33

combination with the parent taxonomic treatment UUID as identifiers for the published

material citation.

The TreatmentBank UUID for the material citation is reused in GBIF as a couple of

treatment UUID * material citation UUID:

Identifier = 03A10B47FFDFFFAFFDE0FA60FB18F865.mc.3B60B00CFFD1FFAFFF38

FED7FD4AFE22

In the Biodiversity Data Journal, the material citations are exported to Darwin Core Archive

and indexed by GBIF automatically on the date of publication. The internal material citation

UUID is minted and entered in the “occurrenceID” of Darwin Core. If the “occurrenceID” is

already occupied by the original ID supplied by the author, it should be moved to the

“associatedOccurrences” field of Darwin Core, while the “occurrenceID” field should be

used again for the internal material citation ID provided by the journal.

Example from Biodiversity Data Journal:

<tp:treatment-sec sec-type="materials

<list-item>

<p>

<bold>Type status:</bold>

<named-content content-type="dwc:typeStatus">Holotype</named-content>.

<bold>Occurrence:</bold>

catalogNumber:

<named-content content-type="dwc:catalogNumber">

<ext-link xlink:href="[url]">IFRD9449</ext-link>

</named-content>;

recordedBy:

<named-content content-type="dwc:recordedBy">Liu Yu-Wei</named-content>;

occurrenceID:

<named-content content-type="dwc:occurrenceID">UUID</named-content>;

associatedOccurrences:

<named-content content-type="dwc:associatedOccurrences">

living culture IFRDCC3104

</named-content>

</p>

</list-item>

</list>

</tp:treatment-sec>

Recommendation

Publishers should use unambiguous separators, such as a Unicode character U+2022 “•”,

for the material citations within an article and identify these with UUIDs in the backend

article JATS XML. When material citations represent a holotype or other type specimens,

this specific status, the collecting event and the collection should be tagged unambiguously

in the backend XML to facilitate harvesting and reuse.

34 Agosti D et al

Taxonomic names

Definition

A taxonomic name, or more generally scientific name, is the formal name, that is the

scientific identity, given to a species or, more generally, a taxon, following the rules of

nomenclature and used widely beyond taxonomy to link data to a particular taxon. Although

the concept of scientific names, along with rules on the interrelationships of taxa, was

introduced in the ancient times by Aristotle (c. 350 BC), and subsequently by Voutsiadou et

al. (2017), binomial names were introduced by Linnaeus in 1753 and since then, have

served as a precursor to today’s persistent identifiers. Taxonomic names play different

roles inferred by their position in a publication. In other words, the context of their use

defines their role. A taxonomic name in the treatment’s nomenclature section is the

nominate taxonomic name of that treatment. A taxonomic name used in a treatment citation

of an existing treatment relates that earlier treatment to the nominate treatment, and

represents its taxonomic history; it can also be accompanied with a label indicating

nomenclatural changes such as a synonymy or a new combination. These can be

nomenclatural acts or subjective synonyms. Any mention of a taxon name in any other

section of the article is regarded as a Taxon Name Usage (TNU).

Identifiers for new taxa descriptions and other types of nomenclatural acts, and their online

registration, are used increasingly, and the process is regulated by zoological (ICZN) and

botanical (ICN) codes (Ride et al. 2012, Turland et al. 2018). Currently, registration of

nomenclatural acts, other than new taxa descriptions, as a part of a valid publication,

whether electronic or print, is mandatory only in mycology including palaeomycology.

Registration of identifiers in other disciplines is mandatory only for new taxa descriptions

but not yet for other nomenclatural acts. It is, however, planned for implementation

(Barkworth et al. 2016a, Barkworth et al. 2016b).

The Catalogue of Life (COL) consortium, in a collaboration with the Global Biodiversity

Information Facility (GBIF), aims to provide a global list of accepted names (Garnett et al.

2020, Hobern et al. 2021) by using a combination of automated and manual integration of

existing checklists including large scale checklists such as WoRMs, as well as checklists

originating from individual taxonomic publications submitted to GBIF. At the moment, COL

provides persistent identifiers for taxonomic names but not for taxon concepts. However,

WoRMS provides persistent identifiers for each available name, including higher taxa, in its

infrastructure, Aphia. Aphia uses Life Science Identifiers (LSIDs) as unique and stable

identifiers. TreatmentBank provides a persistent identifier for each available name

annotated in the nomenclature section of a taxonomic treatment in legacy literature, both

for new taxa or re-descriptions. Taxon concept identifiers are planned as part of ChecklistB

ank, a repository and index for taxonomic data. The taxonomic name for a taxon, which

can include a large number of taxonomic name usages (e.g. synonyms), is separated from

their role in nomenclature (Hobern et al. 2021) and in a subsequent section in the

treatment after the nomenclature section.

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 35

The National Centre for Biotechnology Information (NCBI) taxonomy database holds

unique identifiers (taxIDs) for taxonomic names for which sequence data is available at the

INSDC (Schoch et al. 2020). All records at INSDC have their taxonomic information linked

to the NCBI taxIDs. This database, however, does not comprise a complete list of

taxonomic names. The BOLD taxonomy browser also contains entries for taxonomic

names, with associated identifiers. The ChecklistBank allows mapping of these identifiers

to the entries in COL.

What are the identifiers for new names or nomenclatural acts

Fungi

Pre-publication registration of identifiers for names, typifications and other nomenclatural

acts is mandatory for fungi since 1st January 2013. The identifiers must be published in the

protologue or in nomenclatural changes.

Living vascular plants: IPNI (International Plant Names Index)

In botany, the registration of nomenclatural acts was accepted at the XIX International

Botanical Congress in Shenzhen 2017 (Turland et al. 2018).

Post-publication indexing is a well-established practice of the IPNI which covers seed

plants, ferns and lycophytes, but not bryophytes or algae. IPNI is produced collaboratively

by The Royal Botanic Gardens, Kew, The Harvard University Herbaria, and The Australian

National Herbarium and is hosted by the Royal Botanic Gardens, Kew. Pre-publication

indexing and inclusion of IPNI record identifiers in the publication was first implemented by

the Pensoft journal PhytoKeys (Penev et al. 2016), and later on by EJT. IPNI provides

nomenclatural information (spelling, author, types and first place and date of publication)

for the scientific names of non-fossil vascular plants from family down to infraspecific

ranks, including an index of authors for all the groups under the International Code of

Nomenclature for algae, fungi, and plants (ICNafp).

Algae

PhycoBank is the registration system for nomenclatural acts (new names, new

combinations and types) of algae (Kusber et al. 2019). However, the registered identifiers

are not required to be listed in the original publication.

Fossil plants (except for fossil fungi and diatoms)

Pre-publication indexing is established in the Fossil Plant Names Registry (FPNR) and the

International Fossil Plant Names Index (IFPNI). Registration of taxa is not mandatory.

Bryophytes

IDs for new bryophyte names can be obtained from the Index of Mosses Database

(W³MOST).

36 Agosti D et al

Animals

ZooBank provides registration of new nomenclatural acts, published works, and authors. It

is an authoritative online, open-access, community-generated registry for zoological

nomenclature provided as a service to taxonomists, biologists, and the global biodiversity

informatics community. It is also the official register of the International Commission on

Zoological Nomenclature (ICZN).

The registration of Type Specimens is allowed in Zoobank but yet not fully implemented.

Registration is mandatory for electronic publications publishing new nomenclatural acts

since 1st January 2012. Each electronic publication receives an identifier (LSID) minted by

ZooBank.

Identifiers for taxa in Catalogue of Life, NCBI taxonomy, and TreatmentBank

The Catalogue of Life and the NCBI taxonomy are two widely used reference taxonomies.

Both issue taxon name IDs. For references in articles, authors can use hyperlinked taxon

IDs of either COL or NCBI just as they use sequence accession numbers.

TreatmentBank mints persistent identifiers for taxonomic names as part of the annotation

and FAIRizing of treatments in legacy literature. They are a combination of the treatment

UUID extended with “.taxon”.

How to discover identifiers of names

The following web sites provide the search facility for discovering the identifiers of names.

Fungi

https://www.mycobank.org

Living vascular plants

International Plant Names Index (IPNI)

Algae

https://www.phycobank.org

Fossil plants (except fossil fungi and diatoms)

IFPNI (International fossil plant names index)

PFNR (Plant Fossil Names Registry)

Animals

Zoobank.org

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 37

Identifiers of nomenclatural acts can also be found through other services, for example the

World Register of Marine Species www.marinespecies.org.

Catalogue of Life

https://www.checklistbank.org/tools/name-match

Via Catalogue of Life UI (advanced name search):

https://www.catalogueoflife.org/data/search?q=Pardosa+zyuzini

Via Catalogue of Life API (name usage search):

https://api.catalogueoflife.org/dataset/3LR/nameusage/search?q=Pardosa+zyuzini

Via GBIF UI (species search):

https://www.gbif.org/species/search?q=Pardosa+zyuzini (results include list of other

identifiers)

Via GBIF API (species search):

https://api.gbif.org/v1/species?name=Pardosa+zyuzini (requires further matching to pick

desired identifiers, e.g. ZooBank UUID of name)

NCBI taxonomy

https://www.ncbi.nlm.nih.gov/taxonomy

TreatmentBank

Identifiers for taxonomic names can be found using TreatmentBanks stats https://

tb.plazi.org/GgServer/srsStats

How to mint an identifier for new names

Fungi

Mycobank is an on-line database aimed as a service for the mycological and scientific

community by documenting mycological nomenclatural novelties, that is, new names and

combinations, and associated data such as descriptions and illustrations.

Index Fungorum, the global fungal nomenclator coordinated and supported by the Index

Fungorum Partnership, contains names of fungi including yeasts, lichens, chromistan

fungal analogues, protozoan fungal analogues and fossil forms, at all ranks. As a result of

changes to the ICN relating to registration of names, Index Fungorum provides a

mechanism to register names of new taxa, new names, new combinations and new

typifications.

38 Agosti D et al

Authors of novel fungal taxa must register the new names in only one registry, e.g. either in

MycoBank or Index Fungorum or Fungal Names. These registries regularly coordinate

sharing of data and have arranged an informal agreement to only accept the first listed

name in case it appears in more than one registry. Registration of the same new name in

multiple registries is considered an inappropriate practice that creates a considerable

amount of confusion and extra work for the registries and necessitates the deprecation of

the duplicated registrations at a later stage.

Living vascular plants

IPNI(International Plant Names Index)uses LSIDs as unique identifiers for plant names and

provides a mechanism to register those LSIDs. IPNI records LSIDs for names of new taxa,

new combinations and replacement namesfor living and vascular plants. LSIDs are not

mandatory for valid publication of a plant name. However, if an IPNI LSID is needed, it can

be pre-registered on the IPNI website. For new taxa, the holotype data can also be

provided. The new plant name will be provided with a LSID that will be activated once the

article is published. It is important to note that IPNI can only provide LSIDs for “vascular

plants”, i.e., extant ferns, lycophytes and seed-bearing plants. Thus, IPNI will not give

LSIDs for fungi, bryophytes (mosses), macroalgae (Rhodophyceae etc.), diatoms, or any

fossil vascular plant.

Algae

PhycoBank is the registration system for nomenclatural acts such as new names, new

combinations and types of algae (Kusber et al. 2019). However, it is not required as a part

of valid publication. PhycoBank provides a user interface for curatorial and voluntary data

entry. Each nomenclatural act according to the provisions of ICN Art. 7 is identified by a

stable http identifier that links directly into the PhycoBank portal. The identifier is generated

automatically when a reference is linked to a scientific name. Preparation of a record can

be done while the manuscript is in the review process. If the preparation is not public, a

registration identifier in a manuscript will return the status ‘in preparation’. Curation can be

done once the publication is finalised and reference details like page numbers and volume

are available. The registration can be published on PhycoBank once the scientific paper is

published.

Fossil plants (except fossil fungi and diatoms)

PFNR (Plant Fossil Names Registry) is a database of preferably new names, but also

previously published names of plant fossils and associated nomenclatural acts excluding

fossil diatoms and fossil fungi. It is run by the National Museum Prague for the International

Organisation of Palaeobotany. A LSID links the name to its original publication. The

registration of a new nomenclatural act results in a registration number that is added to the

manuscript. This part is not public and, if necessary, all data can be changed during

manuscript processing. These data are available only to the account owner who registered

the manuscript, and to the editors of the database. When the paper is published, the

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 39

missing data should be added and completed. A more detailed guide for name and

typification registration is available.

IFPNI (International fossil plant names index) is a comprehensive literature-based record of

the scientific names of all fossil plants, algae, fungi, allied prokaryotic forms, protists

(ambiregnal taxa) and microproblematica. IFPNI provides an authoritative online, open-

access, community-sourced registry of fossil plant nomenclature as a service to the global

scientific community. A dynamic database documents all nomenclatural novelties including

new scientific names of extinct organisms and associated data, including registration of the

scientific publications containing nomenclatural acts and author-generated taxonomic

literature in palaeobotany and palaeontology. IFPNI issues LSIDs for each kind of data

object to locate biologically significant data over a network. LSIDs are designed to be

automatically machine resolvable. Read more about IFPNI coverage.

Animals

To obtain a LSID for a new publication or a new name, the article has to be pre-registered

in Zoobank by filling in a form with all the metadata: type of publication, article or

monograph in a series, date of publication, authors, full title, ISSN of the journal, DOI of the

article, volume, number, pages, online archive (Penev et al. 2016). Tutorials are available

online on the Zoobank website to register a publication, a new name, an existing record,

etc.

How to annotate and cite a taxon name

In JATS/TaxPub

Examples of annotations

Fungi

The new fungal species Neopestalotiopsis rhapidis Qi Yang & Yong Wang bis, sp. nov.,

published in Biodiversity Data Journal ( Yang et al. 2021) has the identifier “MycoBank

840065” which resolves to the MycoBank record for this new name, available after logging

in MycoBank.

In the article JATS XML, this record is annotated as:

<tp:taxon-treatment>

<tp:nomenclature>

<tp:taxon-name>

<tp:taxon-name-part taxon-name-part-type="genus">

Neopestalotiopsis

</tp:taxon-name-part>

<tp:taxon-name-part taxon-name-part-type="species">rhapidis</tp:taxon-name-part>

40 Agosti D et al

</tp:taxon-name>

<tp:taxon-authority>Qi Yang & Yong Wang bis</tp:taxon-authority>

<tp:taxon-status>sp. nov.</tp:taxon-status>

</tp:nomenclature>

</tp:taxon-treatment>

Living vascular plants

The new plant speciesArdisia whitmorei Julius & Utteridge, sp. nov. published in

PhytoKeys ( Julius and Utteridge 2022) bears the IPNI ID in the protologue: urn:lsid:ipni.

org:names:77302868-1. The IPNI ID is directly linked to the IPNI record.

In the article JATS XML, this record is annotated as:

<tp:taxon-treatment>

<tp:nomenclature>

<tp:taxon-name>

<tp:taxon-name-part taxon-name-part-type="genus" reg="Ardisia">

Ardisia

</tp:taxon-name-part>

<tp:taxon-name-part taxon-name-part-type="species" reg="whitmorei">

whitmorei

</tp:taxon-name-part>

</tp:taxon-name>

</tp:nomenclature>

</tp:taxon-treatment>

Algae

The new algae Halamphora kenderoviana Zidarova, P.Ivanov, Dzhembekova, M.de Haan

& Van de Vijver, published in PhytoKeys (Zidarova et al. 2022) has the “PhycoBank

103140” identifier which resolves to the PhycoBank record for this name.

In the JATS XML of the article, this record is annotated as:

<tp:taxon-treatment>

<tp:nomenclature>

<tp:taxon-name>

<named-content content-type="phycobank"

xlink:href="https://www.phycobank.org/103140">

Phycobank 103140

</named-content>

<tp:taxon-name-part taxon-name-part-type="genus" reg=" Halamphora">

Halamphora

</tp:taxon-name-part>

<tp:taxon-name-part taxon-name-part-type="species" reg="kenderoviana">

kenderoviana

</tp:taxon-name-part>

</tp:taxon-name>

<tp:taxon-authority>

Zidarova, P.Ivanov, Dzhembekova, M.de Haan & Van de Vijver

</tp:taxon-authority>

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 41

<tp:taxon-status>sp. nov.</tp:taxon-status>

</tp:nomenclature>

</tp:taxon-treatment>

Animals

A new species of giant Eunice, Eunice dharastii published in Zanol and Hutchings (2022)

(https://doi.org/10.3897/zookeys.1118.86448). The taxonomic name resolves at Zoobank

with the LSID urn:lsid:zoobank.org:act:63BC2367-9654-45DA-8021-FD17584DFFDC.

In the article, the JATS XML is annotated as follows:

<tp:nomenclature>

<tp:taxon-name>

BFC45050-4831-5B2D-9E7C-F99DC97D5DF1

</object-id>

xlink:href="https://zoobank.org/63BC2367-9654-45DA-8021-FD17584DFFDC">

63BC2367-9654-45DA-8021-FD17584DFFDC

</object-id>

<tp:taxon-name-part taxon-name-part-type="genus" reg="Eunice">

Eunice

</tp:taxon-name-part>

<tp:taxon-name-part taxon-name-part-type="species" reg="dharastii">

dharastii

</tp:taxon-name-part>

</tp:taxon-name>

<tp:taxon-status>sp. nov.</tp:taxon-status>

</tp:nomenclature>

Expression of links to taxon names in JATS from the Catalogue of Life and NCBI

Taxonomy

The link to Formica rufa in the Catalogue of Life is as follows:

https://www.catalogueoflife.org/data/taxon/6JGM9

</object-id>

The link to Formica rufa taken from the NCBI taxonomy

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=258706

</object-id>

Links to other taxon specific catalogues can be added by entering a respective content-

type.

Linking a taxonomic name anywhere in the text to the taxonomic name in the respective

treatment, an id and <xref rid> element can be included.

42 Agosti D et al

<tp:taxon-treatment>

<tp:nomenclature>

<tp:taxon-name id="tn1">

Formic rufa

C41B87B7-C473-EE75-A7E8-8565FCE1A945.taxon</object-id>

</tp:taxon-name>

</tp:nomenclature>

...

</tp:taxon-treatment>

In a following section of the same article

<sec>

<title>Conclusions</title>

<p>

In this study,

<tp:taxon-name>

Formica rufa

C41B87B7-C473-EE75-A7E8-8565FCE1A945.taxon</object-id>

</tp:taxon-name>

</xref>

is different from Formica rufa sensu Collingwood, 1966.

</p>

</sec>

Recommendation

Provide a pre-publication registration and include identifiers of new taxa or nomenclatural

acts in the original article whenever possible, even when this is not required by a Code.

Where and how to register new taxa and get identifiers for different groups of organisms

such as algae, fungi, plants, or animals is explained in the sections above.

Specimens

Definition

Physical specimens held in collections may be cited directly, for example, material citations

as part of taxonomic treatments, or in other sections of the article. In other cases, data

derived from the specimens such as genetic sequences may include a reference to the

specimen source. To keep track of the use of these specimens, collections should assign

them with at least locally, but better with globally unique IDs (catalogue numbers)* . For

this reason, the Darwin Core (DwC) triplet comprising the catalogue number, collection

code and institution code is often used to assign an ad hoc PID to a specimen. However,

while the DwC triplets are used commonly, they are far from perfect as these codes are

poorly standardised and can change over time (Guralnick et al. 2015).

Specimens are often cited by combinations of metadata other than the DwC triplet, such as

a who-what-when-where combination, e.g. a specimen “X”, collected in locality “Y” by

Recommendations for use of annotations and persistent identiﬁers in taxonomy ... 43

collector “Z” on date XX-YY-ZZZZ, belonging to Taxon A, identified by Person “B”. This may

include names of the person(s) who collected it, where and when this happened and/or a

taxonomic identification. A field number may also be used, which acts as a unique identifier

for the collection event as minted by the collectors. These numbers are not unique beyond

this narrow context and may not have a systematic syntax. The combination of these

properties may allow a specimen to be uniquely identified, but this is not a trivial task and

natural language processing as well as disambiguation efforts are required.

Increasingly, the aim is to keep track of physical specimens through digital twins, called

Digital or Extended Specimens (Hardisty et al. 2019, Lannom et al. 2020, Addink and

Hardisty 2020, Hardisty et