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taxpub's Introduction

DOI

TaxPub Extension of the Journal Publishing Tag Set NISO JATS Version 1.3 (ANSI/NISO Z39.96-2021)

TaxPub is an extension of the JATS Publishing DTD, ANSI/NISO JATS Version 1.3 for encoding of articles containing taxonomic treatments or other taxonomy specific features (e.g., taxonomic names, material citations, etc...)

Tag Libraries

TaxPub V1.0 Tag Library: includes models for TaxPub elements and attributes as well as those from JATS 1.3 Publishing

The Journal Publishing Tag Library for NISO JATS Version 1.3 : Provides extensive documentation including definitions and models for the "generic" elements and attributes in the JATS 1.3 Publishing tag set which TaxPub extends.

Usage

  • Download release, point instance to file tax-treatment-NS0-v1.dtd using Formal Public Identifier:

-//TaxPub//DTD Taxonomic Treatment Publishing DTD v1.0 20230203//EN

  • A single file "flattened" version of the TaxPub V1.0 DTD, tax-treatment_NS0_v1_flat.dtd, derived using the DTDAnalyzer program dtdflatten, may also be used.

Publications About TaxPub

  • Catapano T. 2010. TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions. Journal Article Tag Suite Conference (JATS-Con) Proceedings 2010 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010. Available from: http://www​.ncbi.nlm.nih​.gov/books/NBK47081/

  • Penev L, Catapano T, Agosti D, et al. Implementation of TaxPub, an NLM DTD extension for domain-specific markup in taxonomy, from the experience of a biodiversity publisher. In: Journal Article Tag Suite Conference (JATS-Con) Proceedings 2012 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2012. Available from: http://www.ncbi.nlm.nih.gov/books/NBK100351/

taxpub's People

Stargazers

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Watchers

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Forkers

pensoft ianmulvany daniel-mietchen berlangaluisj teodorgeorgiev

taxpub's Issues

Proposal for identification key attributes

Pensoft proposes the following new values for the content-type attribute to markup the different parts of identification keys:

  • lead
  • lead-to
  • thesis-desc
  • antithesis-desc

The usage is as shown below. The couplet number is marked as 'lead'.
Each couplet 'leads-to' either another couplet or a taxon name.

<tr>
    <td content-type="lead" id="KEY1.1">1</td>
    <td content-type="thesis-desc">Cheek with 3 ...</td>
    <td content-type="lead-to"><xref ref-type="other" rid="KEY1.2">2</xref></td>
</tr>
<tr>
    <td content-type="lead">–</td>
    <td content-type="antithesis-desc">Cheek with 5 ...</td>
    <td content-type="lead-to"><xref ref-type="other" rid="KEY1.4">4</xref></td>
</tr>
<tr>
    <td content-type="lead" id="KEY1.2">2</td>
    <td content-type="thesis-desc">Lines ...</td>
    <td content-type="lead-to"><xref ref-type="other" rid="KEY1.3">3</xref></td>
</tr>
<tr>
    <td content-type="lead">–</td>
    <td content-type="antithesis-desc">Spots...</td>
    <td content-type="lead-to">
        <italic>
            <tp:taxon-name>
                <tp:taxon-name-part taxon-name-part-type="genus">Xanthichthys</tp:taxon-name-part> 
                <tp:taxon-name-part taxon-name-part-type="species">greenei</tp:taxon-name-part>
            </tp:taxon-name>
        </italic>, new species</td>
</tr>

loosen model of nomenclature-citation

current model:

(tp:taxon-name, tp:taxon-author*, (tp:type-genus | tp:type-species)?, 
(mixed-citation | xref)?, tp:material-citation*, tp:taxon-status?, comment?)

expansion of abbreviated genus names

from @pdatascience

... we know that P. damicornis =
Pocillopora damicornis in this context but there is no way to express
it in TaxPub (at least we don’t know how). In the XML we have

<tp:taxon-name>

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

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

</tp:taxon-name>

where to put the full/expanded genus name "Pocillopora"

validation issue: one sec in a treatment enough?

@tcatapano in thsi BDJ, there are treatments that have only one sec in a treatment. https://bdj.pensoft.net/article/6313/element/7/0/viburnum%20lantana/
it seems that this validates, although I thought that the definition of a treatments requires at least two sec?

https://bdj.pensoft.net/article/6313/element/7/0/viburnum%20lantana/

https://bdj.pensoft.net/article/6313/download/xml/

image

and here the one sec treatment in Plazi TB
http://tb.plazi.org/GgServer/html/FEA877B9AE9D425E243213D965AE88D2

loosen model of nomenclature

xmllint and xmlstar (i.e., libxml) throw "non-deterministic" error:

validity error : Content model of nomenclature is not deterministic:
 (sec-meta? , label? , tp:taxon-name , x? , tp:taxon-authority? , x? , 
tp:taxon-status? , x? , 
tp:taxon-identifier* , xref* , x? , tp:nomenclature-citation-list* , x? , 
(tp:type-genus | tp:type-species)? , x? , tp:taxon-type-location? , x?)

Also, the strictness of the model is impeding conversion from GGXML instances and for retrospective encoding in general, which is becoming the primary use case.

Besides, the x thing is nuts

Pensoft: add values to taxon-name-part

Pensoft:

kingdom
subkingdom
phylum
subphylum
superclass
class
subclass
superorder
order
suborder
infraorder
superfamily
family
subfamily
tribe
subtribe
genus
subgenus
section
subsection
speciesAggregate
species
subspecificAggregate
subspecies
variety
subvariety
form
subform
cultivarGroup
cultivar
basionym-authority
taxon-authority
taxon-status (sp. n., comb. n., gen. n., syn. n., stat. n., nomen novum, etc.)
uncertainty-rank (=, ?, cf., aff.)
infraspecific-rank (var., subsp., f.)

DarwinCore + Plazi Additional Ranks:

domain
superkingdom
*kingdom
subkingdom
infrakingdom
superphylum
*phylum
subphylum
superclass
*class
subclass
infraclass
superorder
*order
suborder
infraorder
superfamily
*family
subfamily
infrafamily
supertribe
tribe
subtribe
infratribe
*genus
subgenus
infragenus
section
subsection
series
subseries
speciesAggregate
*specificEpithet
subspeciesEpithet
infraspeciesEpithet
graftChimaeraEpithet
cultivarGroupEpithet
convarEpithet
cultivarEpithet
bioVarietyEpithet
pathoVarietyEpithet
varietyEpithet
subvarietyEpithet
subsubvarietyEpithet
formEpithet
subformEpithet
subsubformEpithet
specialformEpithet
candidateEpithet

define section types (subSubSection types in GG)

@gsautter @tcatapano Following is a list of section types to be included in taxpub, especially for EJT and then implmented in GoldenGateImagine

image

keywords to include all the keywords listed in this section. Ideally they are parsed out and also submitted to BLR

materials_methods Materials and methods is a standard section in scientific papers describing the methods, standards, abbreviations, materials used in the article. This is already introduced, but hardly ever used (at least by me)

results this section describes the results obtained in the study. In taxonomic studies it also includes the treatments.

discussion This section explains the results, puts them in context and draws conclusion (sometimes its own subSubSection. In EJT it has subSubSubSections which are not generic put specific to the article

conservation This section discusses the conservation status of the respective taxon, including often references to RedLists and management plans.

Sections specific to EJT

backmatter includes all the description of the history of the manuscript, distribution of the article

document-head includes all the headers, title, authors, affiliations of the authors, emails, Zoobank numbers. this seems to be the same as frontatter

citation includes the suggested way to cite the article

encoding of proper taxon concept label

from @pdatascience

How would I encode a proper
taxon concept label such as Pocillopora damicornis sec. Poquita-Du et.
Al (2017)?

e.g.,

<tp:taxon-name>

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

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

<to:taxon-name-part taxon-name-part-type=”sec”>sec. Poquita-Du et. Al
(2017)? </tp:taxon-name-part>

</tp:taxon-name>

Pensoft: add values to treatment-sec-type

from taxonX:

  • abstract
  • acknowledgments
  • biology_ecology
  • description
  • diagnosis
  • discussion
  • distribution
  • etymology
  • key
  • introduction
  • materials_examined
  • materials_methods
  • multiple
  • synopsis
  • other

EOL Biodiversity Subjects Ontology

  • Class: Barcode: Description: Links to barcode data, including BOL and others.
  • Class: CitizenScience: Description: Links to citizen science projects relevant to this taxon.
  • Class: Development: Description: Aspects of development in the focal taxon, including ontogenetic changes. This does not include life cycle information.
  • Class: Education: Description: Notes about education
  • Class: EducationResources: Description: Links to education resources relevant to this taxon.
  • Class: FossilHistory: Description: A description of the known fossil history of the taxon. Known from what period and in what areas.
  • Class: FunctionalAdaptations: Description: Biomechanics and other descriptions establishing relationships between morphologies, properties, or behaviors and their functions or adaptive significance.
  • Class: Genome: Description: Links to genomic information or full genomes of the focal taxon.
  • Class: IdentificationResources: Description: Links to identification keys or other identification resources that include this taxon.
  • Class: Notes: Description: A category intended as a place to map content that is difficult to fit into EOL subchapters or because it contains content intended for a wide variety of subchapters.
  • Class: NucleotideSequences: Description: Links to sources of nucleotide sequences, including DNA, RNA, fragment length polymorphisms, SNP's, microsatellites, etc.
  • Class: SystematicsOrPhylogenetics
    Description: Description of the evolutionary relationships of this taxon and any controversies or important changes in the understanding of relationships. Also descriptions of any systematic or phylogenetic treatments of the taxon.
  • Class: Taxonomy: Description: Information about taxonomic history, nomenclatural issues.
  • Class: TypeInformation: Description: Information about type specimens associated with a given taxon; e.g., label data, the collection where they are stored, information about the specimens' history, etc.

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