Common query/response model

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Pilot No 2.

Common query/response model for automated registration of higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank)

Person leading the pilot: Lyubomir Penev - Pensoft

Institutions involved in the pilot: IPNI (Nicola Nicolson) ZooBank (Richard Pyle) Index Fungorum (Paul Kirk) MycoBank (Vincent Roberts)


First draft by: Lyubomir Penev, Teodor Georgiev, Pavel Stoev

Contributions from: Paul Kirk, Christine Barker, Vincent Roberts, Rich Pyle


Introduction

The process of post-publication recording and indexing of taxonomic and nomenclatural acts has a long tradition, in some cases dating as far back as the middle of 19th century. As a result, we have available for use several historical indexes, for example, Index Kewensis in botany, Index Fungorum in mycology, and Zoological Record and Index Animalium in zoology. With the appearance of the Internet and the opportunity to publish taxonomic novelties online, the process of post-publication recording brought into focus the concept of pre-publication registration. The different options of such registration and the relationship to the process of publishing have been extensively reviewed by Pyle and Michel (2008) and elsewhere.

Electronic registration of nomenclatural acts in trusted online registries is a dynamic process which still needs to be elaborated in accordance with the latest developments in the biological Codes using the opportunities of constantly developing Web technologies. Despite the current progress five major questions remain to be answered: (1) When exactly should the registration of a nomenclatural act take place – before or after publication? (2) Who should be responsible for the registration of the act – authors, registry curators or publishers? (3) Who should validate the record at the registry? (4) Who validates the accuracy of the bibliographic metadata for any registered act? (5) What is the official date the nomenclature act becomes effectively published in cases of a joint electronic and printed publication?

The International Botanical Congress in Melbourne in July 2011 had a major impact on streamlining the process by amending the International Code of Nomenclature for algae, fungi, and plants (ICNafp) such that, from 1 January 2013 to be validly published all new names of fungi must be registered before publication and identifiers for each name included in the publication (Miller et al. 2011, Knapp et all. 2011).

Shortly thereafter, The International Commission of Zoological Nomenclature has voted in favour of a revised version of the amendment to the International Code of Zoological Nomenclature that first was proposed in 2008. The purpose of the amendment is to expand and refine the methods of publication allowed by the Code, particularly in relation to electronic publication. The amendment establishes an Official Register of Zoological Nomenclature (with ZooBank as its online version), allows electronic publication after 2011 under certain conditions, and disallows publication on optical discs after 2012. The requirements for electronic publications are that the work be registered in ZooBank before it is published, that the work itself state the date of publication and contain evidence that registration has occurred, and that the ZooBank registration state both the name of an electronic archive intended to preserve the work and the ISSN or ISBN associated with the work. Registration of new scientific names and nomenclatural acts is not required. The Commission has confirmed that ZooBank is ready to handle the requirements of the amendment [International Commission of Zoological Nomenclature (ICZN) 2012].

The current situation with registration in the three domains of eukaryotic organisms can be summarized as follows:

FUNGI

  • Pre-publication registration mandatory for fungi since 1st of January 2013
  • Record identifiers must be published in the protologue
  • Three official registries approved: MycoBank, Index Fungorum, Fungal Names

PLANTS

  • Post-publication indexing is a well-established practice of IPNI
  • Mandatory pre-registration and inclusion of record identifiers in protologues pioneered by PhytoKeys

ANIMALS

  • Post-publication registration is a well-established practice of Zoological Record
  • Pre-publication registration at ZooBank mandatory since 1st of January 2012 for e-only
  • Record identifiers (LSIDs) should be published in the original description

The present report deals with a specific and important part of the registration process, namely a common model and associated workflow between publishers and registries in further streamlining the process of registration and making it cost efficient through automated, server-to-server querying.


Which taxonomic and nomenclatural acts are subject of registration?

There are significant differences in the scope and number of taxonomic and nomenclatural acts that are tracked by the current registries (Table 1). In general, there are two types of registered acts, namely Code-governed (e.g., new names, lectotypifications, neotypifications, epitypifications, replacement names, etc.) and other acts that are important for taxonomy, but are not regulated by the Code (e,g., re-descriptions, revisions, and some other taxonomic treatments).

In several cases, acts are treated differently by the biological Codes. For example, new suprafamilial names and new combinations are governed by the ICNafp, but not by ICZN.


Table 1. Nomenclatural acts that are recorded by the indexing services and could potentially be a subject of registration in botany, mycology and zoology

Taxonomic/nomenclatural act IPNI Index Fungorum MycoBank ZooBank
Description of a new taxon: Example Example Example Example
- suprafamilial X + +
- familial X + + +
- infrafamilial X + + +
- generic X + + +
- infrageneric X + + +
- specific X + + +
- infraspecific X + + +
- hybrids1 X + + n/a
New replacement name + +
New synonym +
New combination + + +
Removal from synonymy +
Tautonym2 + n/a
Typifications3
- lectotype (+) + +
- neotype (+) + +
- epitype (+) + + n/a

1 Hybrids need not be treated as a category of new taxon, but there needs to be a mechanism of flagging the ranks above as hybrids where necessary. 2 Tautonyms are not validly published in ICNafp. IPNI (and IF) record tautonyms if published, but such cases should be picked up at registration stage. 3 IPNI normally does not record new typifications.


The registration workflow

The registration process proposed in the current report is “journal-centric”, and has already been tested in the Pensoft’s journals ZooKeys, PhytoKeys and MycoKeys. ZooKeys was the first journal to provide a mandatory in-house registration in ZooBank on behalf of the authors for all new taxa described in the journal and citation of their respective LSIDs in the original publication. Since its launch in 2008, ZooKeys has contributed about one third of all names currently registered in ZooBank. This policy has been followed by its sister journals PhytoKeys and MycoKeys where likewise all nomenclatural acts were supplied to the International Plant Name Index (IPNI) for plants and MycoBank and Index Fungorum for fungi. In our view, the registration of nomenclatural acts and the quality control of the bibliographic metadata in these registries should be a primary responsibility of publishers and, to a lesser extent, of authors or registry curators. Moreover, the publishers’ role is becoming even more essential in the latest stage of the registration, specifically checking and correcting (in the case of fungi, as defined in the ICNafp) the pre-publication registration details against the finally published information. In addition, we also believe that registration of nomenclatural acts should be mandatory for all groups, no matter whether they are published on paper or in a digital format, especially for those groups for which this is not yet mandatory under the relevant Code.

In our model, the registration of taxonomic and nomenclatural acts could be done by three main groups: (1) authors, (2) registry curators, and (3) publishers (Figure 1), hence the workflow is based on a multiple-choice principle.

In case a publisher takes the responsibility for the registration of taxonomic and nomenclatural acts in the above mentioned electronic registries, the workflow can be performed following a common model (Fig. 2):

Step 1. XML query to from the publisher to the the registry in the day of acceptance of the manuscript (containing the type of act, taxon names, and preliminary bibliographic metadata)

Step. 2a. Responce XML report containing the unique identifier (e.g., LSID, PURL, or other resolvable URLs) of the act and potential error messages

Step. 2b. Error correction and de-duplication performed manually: human intervention, at either registry’s or publisher’s side (or at both)

Step. 3. Inclusion of identifiers in the published treatments (protologues, nomenclatural acts)

Step 4. Final XML report sent by publisher on the day of publication (exact bibliographic details of the published article: authors, title, journal, issue no, date of publication, pagination)



There are several reasons to maximize automation of registration, the most significant being:

  • Increasing cases of bulk descriptions of new taxa within a single paper, sometimes counted in hundreds, which creates significant overhead on the authoring and editorial process
  • Decreased risk of errors caused by human intervention (e.g. re-typing)
  • Disambiguation of the dates of acceptance and publication of a manuscript
  • Efficient and accurate validation of final published data and metadata through automated export from the publisher to the registry on the day of publication


The registration process in practice

Within the framework of the EU FP7 project pro-iBiosphere, and in close collaboration with Zoological Record, ZooBank, IPNI, MycoBank and Index Fungorum, as well as with the Global Names Project we are elaborating a workflow and associated software tools to streamline the registration of nomenclatural acts within the pre-publication process. The workflow will be implemented through the currently developed Pensoft Writing Tool (PWT).

The Pensoft Writing Tool is a collaborative, crowd-sourcing platform, designed for writing, pre-submission markup and submission of academic articles. PWT is a part of the TRIADA publishing platform of Pensoft and integrates with some other tools of it, such as the Pensoft Markup Tool (PMT), Pensoft Journal System (PJS) and Pensoft Taxon Profile (PTP).

To make possible the automated pre-publication registration, the PWT provides predefined, Codes-compliant templates for different kinds of taxonomic and nomenclatural acts, such as new taxa descriptions, new combinations, synonymies, etc. The tool ensures availability check of taxon names during the preparation process and automated registration of taxonomic and nomenclatural acts in the electronic registries MycoBank, Index Fungorum, IPNI, ZooBank, once the manuscript is accepted for publication.

The PWT automatically detects which index to contact depending on to which group (at kingdom or phylum level) a taxonomic treatment belongs.

Implementation of the PWT and similar XML-based tools will facilitate the process of publication and dissemination of biodiversity information. It will pave the way for unification and streamlining the registration process, even more to building the next-generation e-infrastructure for a common global taxon names registry.


Automated registration with the International Plant Name Index (IPNI)

The pre-publication registration of new plant taxa and nomenclatural acts in IPNI and inclusion of the IPNI identifiers in the protologues has first been invented by the journal PhytoKeys since the publication of its first issue in 2010 (Penev et al. 2010). With the pro-iBiosphere project the workflow has been piloted to include automated registration module. Here are some samples of the XML server-to-server query model established between IPNI and PhytoKeys, illustrated by a new genus Lettowia description and new combination Lettowia nyassae (Oliv.) H. Rob., comb. nov. in the paper of Robinson and Skvarla (2013):


XML Query

The following XML query is sent from Pensoft Efitorial Office to IPNI on the day of acceptance of the manuscript for publication:

<?xml version="1.0" encoding="utf-8"?> <ipni-query>

   <taxon-acts>
  	 <taxon-act ID="1" article_id="5556" type="tax_nov">
  		 <taxon-rank>generic</taxon-rank>
  		 <taxon-parent>
  			 <kingdom>Plantae</kingdom>
  			 <order>Asterales</order>
  			 <family>Asteraceae</family>
  		 </taxon-parent>
  		 <taxon-name>
  			 <taxon-name-part part="genus">Lettowia</taxon-name-part>
  		 </taxon-name>
  		 <basionym-author/>
  		 <publishing-author>H. Rob. & Skvarla</publishing-author>
  		 <description-language>English</description-language>
  		 <hybrid type="no"/>
  		 <type type="name">
  			 <taxon-name>
  				 <taxon-name-part part="genus">Vernonia</taxon-name-part>
  				 <taxon-name-part part="species">nyassae</taxon-name-part>
  			 </taxon-name>
  			 <publishing-author>Oliv.</publishing-author>
  			 <basionym-author/>
  			 <publication>
  				 <journal-name>Icon. Pl.</journal-name>
  				 <year>1881</year>
  				 <volume>14</volume>
  				 <issue>2</issue>
  				 <page>36</page>    
  			 </publication>
  		 </type>
  		 <published-in>
  			 <journal-name>PhytoKeys</journal-name>
  			 <year>2013</year>
  			 <title>Lettowia, a new genus of Vernonieae from East Africa (Asteraceae)</title>
  			 <issue>25</issue>
  			 <taxon-page>48</taxon-page>
  			 <start-page>47</start-page>
  			 <end-page>53</end-page>
  			 <publication-date>19-07-2013</publication-date>
  			 <doi>10.3897/phytokeys.25.5556</doi>
  		 </published-in>
  	 </taxon-act>
  	 <taxon-act ID="2" article_id="5556" type="comb_nov">
  		 <taxon-rank>specific</taxon-rank>
  		 <taxon-parent>
  			 <kingdom>Plantae</kingdom>
  			 <order>Asterales</order>
  			 <family>Asteraceae</family>
  		 </taxon-parent>
  		 <taxon-name>
  			 <taxon-name-part part="genus">Lettowia</taxon-name-part>
  			 <taxon-name-part part="species">nyassae</taxon-name-part>
  		 </taxon-name>
  		 <basionym-author>Oliv.</basionym-author>
  		 <publishing-author>H. Rob.</publishing-author>
  		 <hybrid type="no"/>
  		 <basionym rank="specific">
  			 <taxon-name>
  				 <taxon-name-part part="genus">Vernonia</taxon-name-part>
  				 <taxon-name-part part="species">nyassae</taxon-name-part>
  			 </taxon-name>
  			 <basionym-author>Oliv.</basionym-author>
  			 <publication>
  				 <journal-name>Icon. Pl.</journal-name>
  				 <year>1881</year>
  				 <volume>14</volume>
  				 <issue>2</issue>
  				 <page>36</page>    
  			 </publication>
  		 </basionym>
  		 <published-in>
  			 <journal-name>PhytoKeys</journal-name>
  			 <year>2013</year>
  			 <title>Lettowia, a new genus of Vernonieae from East Africa (Asteraceae)</title>
  			 <issue>25</issue>
  			 <taxon-page>50</taxon-page>
  			 <start-page>47</start-page>
  			 <end-page>53</end-page>
  			 <publication-date>19-07-2013</publication-date>
  			 <doi>10.3897/phytokeys.25.5556</doi>
  		 </published-in>
  	 </taxon-act>
   </taxon-acts>

</ipni-query>

XML Response

IPNI generated the following responce to the request containing the registration numbers of both the new genus name and the new combination:

<?xml version="1.0" encoding="UTF-8" standalone="yes" ?> <ipni-query>

   <taxon-acts>
  	 <taxon-act article_id="5556" ID="1" type="tax_nov">
  		 <basionym-author />
  		 <description-language>English</description-language>
  		 <hybrid type="no" />
  		 <ipni-id>77130232-1</ipni-id>
  		 <published-in>
  			 <doi>10.3897/phytokeys.25.5556</doi>
  			 <end-page>53</end-page>
  			 <issue>25</issue>
  			 <journal-name>PhytoKeys</journal-name>
  			 <publication-date>19-07-2013</publication-date>
  			 <start-page>47</start-page>
  			 <taxon-page>48</taxon-page>
  			 <title>Lettowia, a new genus of Vernonieae from East Africa (Asteraceae)</title>
  			 <year>2013</year>
  		 </published-in>
  		 <publishing-author>H. Rob. & Skvarla</publishing-author>
  		 <taxon-rank>generic</taxon-rank>
  		 <taxon-name>
  			 <taxon-name-part part="genus">Lettowia</taxon-name-part>
  		 </taxon-name>
  		 <taxon-parent>
  			 <family>Asteraceae</family>
  			 <kingdom>Plantae</kingdom>
  			 <order>Asterales</order>
  		 </taxon-parent>
  		 <type type="name" />
  	 </taxon-act>
  	 <taxon-act article_id="5556" ID="2" type="comb_nov">
  		 <basionym rank="specific">
  			 <publication>
  				 <issue>2</issue>
  				 <journal-name>Icon. Pl.</journal-name>
  				 <page>36</page>
  				 <volume>14</volume>
  				 <year>1881</year>
  			 </publication>
  			 <taxon-name>
  				 <taxon-name-part part="genus">Vernonia</taxon-name-part>
  				 <taxon-name-part part="species">nyassae</taxon-name-part>
  			 </taxon-name>
  			 <basionym-author>Oliv.</basionym-author>
  		 </basionym>
  		 <basionym-author>Oliv.</basionym-author>
  		 <hybrid type="no" />
  		 <ipni-id>77130233-1</ipni-id>
  		 <published-in>
  			 <doi>10.3897/phytokeys.25.5556</doi>
  			 <end-page>53</end-page>
  			 <issue>25</issue>
  			 <journal-name>PhytoKeys</journal-name>
  			 <publication-date>19-07-2013</publication-date>
  			 <start-page>47</start-page>
  			 <taxon-page>50</taxon-page>
  			 <title>Lettowia, a new genus of Vernonieae from East Africa (Asteraceae)</title>
  			 <year>2013</year>
  		 </published-in>
  		 <publishing-author>H. Rob.</publishing-author>
  		 <taxon-rank>specific</taxon-rank>
  		 <taxon-name>
  			 <taxon-name-part part="genus">Lettowia</taxon-name-part>
  			 <taxon-name-part part="species">nyassae</taxon-name-part>
  		 </taxon-name>
  		 <taxon-parent>
  			 <family>Asteraceae</family>
  			 <kingdom>Plantae</kingdom>
  			 <order>Asterales</order>
  		 </taxon-parent>
  	 </taxon-act>
   </taxon-acts>

</ipni-query>


Automated registration with Index Fungorum

The registration wokf flow of Index Fungorum (IF) will adopt that of IPNI after the IF’s database will move on the IPNI infrastructure at Kew Gardens.


References

International Commission of Zoological nomenclature (ICZN) (2012) Amendment of Articles 8, 9, 10, 21 and 78 of the International Code of Zoological Nomenclature to expand and refine methods of publication. ZooKeys 219: 1-10. doi: 10.3897/zookeys.219.3944

Knapp S, McNeill J, Turland N (2011) Changes to publication requirements made at the XVIII International Botanical Congress in Melbourne - what does e-publication mean for you? PhytoKeys 6: 5-11. doi: 10.3897/phytokeys.6.1960

Miller JS, Funk VA, Wagner WL, Barrie F, Hoch PC, Herendeen P (2011) Outcomes of the 2011 Botanical Nomenclature Section at the XVIII International Botanical Congress. PhytoKeys 5: 1-3. doi: 10.3897/phytokeys.5.1850

Penev L, Kress WJ, Knapp S, Li DZ, Renner S (2010) Fast, linked, and open – the future of taxonomic publishing for plants: launching the journal PhytoKeys. PhytoKeys 1: 1-14. doi: 10.3897/phytokeys.1.642

Polaszek A, Alonso-Zarazaga M, Bouchet P, Brothers DJ, Evenhuis N, Krell F-T, Lyal CHC, Minelli A, Pyle RL, Robinson NJ, Thompson FC, van Tol J (2005) ZooBank: the open-access register for zoological taxonomy: Technical Discussion Paper. Bulletin of Zoological Nomenclature 62(4): 210-220.

Pyle RL, Michel E (2008) ZooBank: Developing a nomenclatural tool for unifying 250 years of biological information. Pp. 39-50. In: Minelli, A., Bonato, L. & Fusco, G. (eds.) Updating the Linnaean Heritage: Names as Tools for Thinking about Animals and Plants. Zootaxa 1950: 1-163.

Robinson H, Skvarla J (2013) Lettowia, a new genus of Vernonieae from East Africa (Asteraceae). PhytoKeys 25: 47-53. doi: 10.3897/phytokeys.25.5556