PhycoBank: Issueshttps://dev.e-taxonomy.eu/redmine/https://dev.e-taxonomy.eu/redmine/redmine/favicon.ico?14691914852019-09-03T14:28:02ZEDIT Project Management
Redmine task #8515 (New): Remaining registation UI taskshttps://dev.e-taxonomy.eu/redmine/issues/85152019-09-03T14:28:02ZAndreas Kohlbecker
<p>This is an overview on some tasks which still need to be done for the registration UI </p>
<ul>
<li>User self registration <a class="issue tracker-5 status-4 priority-10 priority-lowest child" title="feature request: Selfregistration widget (Feedback)" href="https://dev.e-taxonomy.eu/redmine/issues/6170">#6170</a>, <a class="issue tracker-5 status-1 priority-13 priority-high13 child" title="feature request: Selfregistration widget follow up (New)" href="https://dev.e-taxonomy.eu/redmine/issues/10460">#10460</a>, <a class="issue tracker-4 status-5 priority-10 priority-lowest closed child" title="bug: Duplicate user name not handled correctly during registration (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/10461">#10461</a></li>
<li>Password recovery function <a class="issue tracker-5 status-5 priority-10 priority-lowest closed child" title="feature request: Service and webservice to recover forgotten passwords (Closed)" href="https://dev.e-taxonomy.eu/redmine/issues/6161">#6161</a></li>
</ul>
task #8397 (New): Algae Names Index - presentation https://dev.e-taxonomy.eu/redmine/issues/83972019-07-23T10:12:25ZAndreas Kohlbecker
<p>This ticket covers ideas, notes and requirement regarding the presentation of the PhycoBank Index in the portal</p>
task #8102 (New): typedsignations without statushttps://dev.e-taxonomy.eu/redmine/issues/81022019-02-15T16:33:47ZAndreas Kohlbecker
<p>es sind 95 Typedesignations betroffen 6 SpecimenTypeDesignations und 89 NameTypes</p>
<p>most important are the issues listed in </p>
<ul>
<li><a class="attachment" href="https://dev.e-taxonomy.eu/redmine/attachments/1532">select_r_identifier_r_specificIdentifier_n_id_name_id_n_uuid_nam_201902151729-types-missing-status.ods</a> </li>
</ul>
<p>second:</p>
<ul>
<li><a class="attachment" href="https://dev.e-taxonomy.eu/redmine/attachments/1534">select_td_DTYPE_td_uuid_td_typeName_id_tn_titleCache_typifiedNam_201902151732-types-missing-status.ods</a> (93 problem cases)</li>
</ul>
<p>and third the complete list:</p>
<ul>
<li><a class="attachment" href="https://dev.e-taxonomy.eu/redmine/attachments/1533">TypeDesignationBase_201902151722-specimentypes-missing-status.ods</a> (95 problem cases)</li>
</ul>
task #8085 (New): Decide on a data schema to use for submitting nomenclatural acts to the cdm web...https://dev.e-taxonomy.eu/redmine/issues/80852019-02-08T16:13:52ZAndreas Kohlbecker
<p>Digital publishers can send the data for nomenclatural acts (Name, Types, Reference ) to a web service endpoint. </p>
<p>The transport schema of the data (TCS, CDM, ...) needs to be decided.</p>
<ul>
<li>TCS : implementation of the type and specimen part is too limited - REJECTED<br></li>
</ul>
<a name="General-considerations"></a>
<h2 >General considerations<a href="#General-considerations" class="wiki-anchor">¶</a></h2>
<p><strong>Submission of typifications</strong></p>
<p>Publishers may not have highly atomized data for the specimen, this means that the web service needs to accept submissions which only consist of</p>
<ul>
<li>titleCache</li>
<li>type status: (e.g. holotypem, lectotype)</li>
<li>kindOfUnit (default=Specimen)</li>
<li>record basis (default=PreservedSpecimen)</li>
<li>collection code : Index Herbariorum Code (BRM or B or BM or BP etc.); avoid duplicate Collections, reuse existing, create new only if needed</li>
<li>accession number:</li>
</ul>
<p>All fields are required!</p>
task #7891 (New): deduplicate nameshttps://dev.e-taxonomy.eu/redmine/issues/78912018-11-07T15:04:50ZAndreas Kohlbecker
<p>The phycobank db contains 117 cases of potentially duplicate names which need to be checked. See attached spreadsheet<br>
17 of these cases are names which are empty.</p>
<p>Duplicate names can be found by </p>
<pre><code class="sql syntaxhl"><span class="k">SELECT</span> <span class="k">COUNT</span><span class="p">(</span><span class="o">*</span><span class="p">),</span> <span class="n">genusOrUninomial</span><span class="p">,</span> <span class="n">infraGenericEpithet</span><span class="p">,</span> <span class="n">specificEpithet</span><span class="p">,</span> <span class="n">infraSpecificEpithet</span>
<span class="k">FROM</span> <span class="n">TaxonName</span>
<span class="k">GROUP</span> <span class="k">BY</span> <span class="n">genusOrUninomial</span><span class="p">,</span> <span class="n">infraGenericEpithet</span><span class="p">,</span> <span class="n">specificEpithet</span><span class="p">,</span> <span class="n">infraSpecificEpithet</span>
<span class="k">HAVING</span> <span class="k">COUNT</span><span class="p">(</span><span class="o">*</span><span class="p">)</span><span class="o">></span><span class="mi">1</span><span class="p">;</span>
</code></pre> task #7812 (Resolved): Umgang mit invaliden höheren Taxonnamen für die Klassifikationhttps://dev.e-taxonomy.eu/redmine/issues/78122018-10-09T08:32:50ZWolf-Henning Kusber
<p>Bsp.</p>
<p>In Syllabus 1/1: 29</p>
<p>-5. Subclass [Nostocophycidae]</p>
<p>Möglichkeiten:<br>
1) Eintrag als "Nostocophycidae, nom. inval."<br>
2) Weglassen, da invalider Name, es entsteht eine Klassifikationslücke (2. Wahl)<br>
3) Eintrag als Name ohne zusätzliche Zeichen (wäre eine schlechte Lösung, weil wir ein Registrierungssystem, primär für valide Namen haben.</p>
task #7748 (Resolved): Genus name duplicates, Genus without referencehttps://dev.e-taxonomy.eu/redmine/issues/77482018-09-11T12:31:49ZWolf-Henning Kusber
<p>Andreas K.: genus name without reference is duplicate of the same name with reference (13x, highlighted blue and grey) please deduplicate.</p>
<p>Andreas K.: "Diatoms" is a vernacular name for division "Bacillariophyta", what to do?</p>
<p>Henning: Names highlighted in yellow are mentioned in a IAPT registration, but not registered. Reference to be added by Henning.</p>
<p>Henning: Navicula Grunow = Data error for Navicula minuscula var. bahusiensis Grunow, Done.</p>
<p>File also on Y Algenregistrierung DataCleaning</p>
task #7684 (Feedback): meaning of status rejected and according workflowhttps://dev.e-taxonomy.eu/redmine/issues/76842018-08-27T11:16:25ZAndreas Kohlbecker
<p>Henning:</p>
<p>"rejected" mean e.g. User contact Curator, that the manuscript was finally rejected by the Edior. This is the situation, the curator can set the regstrations to "rejected" and a name is not anymore blocked.</p>
task #7012 (In Progress): Workflow with Pensofthttps://dev.e-taxonomy.eu/redmine/issues/70122017-10-09T14:41:42ZAndreas Kohlbecker
<p>Design and establish an partially automated workflow with Pensoft.</p>
<hr>
<p><a name="Interaction-workflow-between-Phycobank-and-Pensoft-Publishers"></a>
<h1 >Interaction workflow between Phycobank and Pensoft Publishers<a href="#Interaction-workflow-between-Phycobank-and-Pensoft-Publishers" class="wiki-anchor">¶</a></h1>
<ul class="toc right"><li><strong>Table of contents</strong></li><li><a href="#Interaction-workflow-between-Phycobank-and-Pensoft-Publishers">Interaction workflow between Phycobank and Pensoft Publishers</a><ul><li><a href="#persistent-registration-identifier">persistent registration identifier</a></li><li><a href="#Authenticationauthorization">Authentication/authorization</a></li><li><a href="#Users-and-roles">Users and roles</a></li><li><a href="#Registration-workflow-states">Registration workflow states</a></li><li><a href="#Curatorial-process-in-the-registration-office">Curatorial process in the registration office</a></li><li><a href="#Initialization-of-the-registration-process">Initialization of the registration process</a></li><li><a href="#Data-scope-and-granularity">Data scope and granularity</a><ul><li><a href="#Name">Name</a></li><li><a href="#Typifications">Typifications</a><ul><li><a href="#Specimen-types">Specimen types</a></li><li><a href="#Name-types">Name types</a></li></ul>
</li></ul>
</li><li><a href="#Receiving-messages-from-Phycobank-during-the-edit-and-curation-process">Receiving messages from Phycobank during the edit and curation process</a></li><li><a href="#Requesting-for-the-status-of-a-registration-record">Requesting for the status of a registration record</a></li><li><a href="#Publishing-a-registration-identifier">Publishing a registration identifier</a></li><li><a href="#Workflow-as-sequence-diagram">Workflow as sequence diagram</a></li><li><a href="#Teleconference-on-July-7th-2019">Teleconference on July 7th 2019</a></li><li><a href="#Open-Questions">Open Questions</a></li></ul></li></ul>
<p><em>The below concept is based on a discussion with Teodor Georgiev (<a href="mailto:preprint@pensoft.net">preprint@pensoft.net</a>) from Pensoft Publishers at the TDWG 2017 conference. This original concept has been reconsidered and was refined during a teleconference on July 7th 2019</em></p>
<p>Phycobank is a repository for registration of algal names and types according to the International Code of Nomenclature for algae, fungi, and plants (ICN). Phycobank will actually create registration for whole nomenclatural acts which can encompass 0 - 1 new scientific names and 0 - n typifications for new or existing names. The different types of typifications cover isosyntype, isotype, lectotype, neotype, paralectotype, paraneotype, paratype, second step lectotype, second step neotype & syntype.</p>
<p>Phycobank aims in establishing a workflow with publishers. Phycobank aims in realizing this interaction for the first time with Pensoft Publishers.</p>
<p>he basic principles of the interaction between Phycobank and Pensoft Publishers as described in this document have been discussed during the "Night at the museum" event at the TDWG conference 2017 (Andreas Kohlbecker, <a href="mailto:a.kohlbecker@bgbm.org">a.kohlbecker@bgbm.org</a>; Teodor Georgiev, <a href="mailto:preprint@pensoft.net">preprint@pensoft.net</a>). The current state of this concept is more elaborated and detailed in contrast to the outcome of the discussion in Ottawa on October, 2017 which has been sent to <a href="mailto:preprint@pensoft.net">preprint@pensoft.net</a> on Oktober 10th 2017</p>
<a name="persistent-registration-identifier"></a>
<h2 >persistent registration identifier<a href="#persistent-registration-identifier" class="wiki-anchor">¶</a></h2>
<p>For interaction with registration web service persistent registration identifier (<code>{phycobankID}</code>) needs to be used in the request URI as url-encoded path element: <code>{phycobankID-urlencoded} = urlencode(http://phycobank.org/{integer})</code></p>
<a name="Authenticationauthorization"></a>
<h2 >Authentication/authorization<a href="#Authenticationauthorization" class="wiki-anchor">¶</a></h2>
<p>The Publisher will need to authenticate at the Phycobank registration webservice via HTTP-Basic authentication. Authorization at Phycobank is established on base of the OAuth 2.0 protocol. </p>
<a name="Users-and-roles"></a>
<h2 >Users and roles<a href="#Users-and-roles" class="wiki-anchor">¶</a></h2>
<p>Phycobank distinguishes two roles which are relevant for the registration process:</p>
<ul>
<li><strong>Submitter</strong>: The user initiating a registration is called <strong>submitter</strong>. Only the <strong>submitter</strong> of a registration can modify the related data. There is always only one submitter per registration. Pensoft will therefore be the <strong>submitter</strong> of all registrations created on behalf of the authors which do submit publications to Pensoft witch contain nomenclatural acts for algae names.</li>
<li><strong>Curation</strong>: The <em>curation</em> of Phycobank can also modify registration data as long the registration is not yet published. </li>
</ul>
<a name="Registration-workflow-states"></a>
<h2 >Registration workflow states<a href="#Registration-workflow-states" class="wiki-anchor">¶</a></h2>
<ul>
<li><code>PREPARATION</code>: Initial state of a new registration</li>
<li><code>CURATION</code>: Once the editing phase of a nomenclatural act is completed, the registration record (new scientific name, typifications) are passed to the curation. This status indicates that a registration is in the curatorial process. As result of this process (for details see paragraph below) the status may be changed to <code>READY</code>, <code>REJECTED</code> (severe unsolvable problem with the nomenclatural act) or even back to <code>PREPARATION</code> (request to fix incomplete, invalid data)</li>
<li><code>READY</code>: The registration record can be published. The publication will immediately happen as soon as the publication date (, doi and pages detail) is set in the data.<br></li>
<li><code>PUBLISHED</code>: Unmodifiable final state of a successful registration. All related data is locked and can no longer be modified.</li>
<li><code>REJECTED</code>: Unmodifiable final state of a failed registration. All related data is locked and can no longer be modified.</li>
</ul>
<a name="Curatorial-process-in-the-registration-office"></a>
<h2 >Curatorial process in the registration office<a href="#Curatorial-process-in-the-registration-office" class="wiki-anchor">¶</a></h2>
<p>The data curator of the registration office will manually validate the registration data once the status is set to <code>CURATION</code>. The curation process may result in one or more of the following actions:</p>
<ul>
<li>Minor problems in the data are corrected by the curator. This includes for example minor orthographic corrections of a new name to be published, atomize specimen data, if necessary; add missing data (e.g. publication date of basionym reference).</li>
<li>Severe problems like that the exact same name has already been published before will lead to rejection of the registration which is expressed by the state <code>REJECTED</code></li>
<li>The registration state is progressed to <code>READY</code> in case of successful validation.</li>
<li>The state returns to <code>PREPARATION</code> in case of problems which can't be solved by the curator without feedback from the author team. The curator will add a curatorial annotation to the registration record with information or questions for the author team. <strong>TODO: This needs to be discussed</strong> <a class="issue tracker-5 status-6 priority-11 priority-default closed" title="feature request: Feedback mechanism from curator to publisher and author team (Rejected)" href="/redmine/issues/8103">#8103</a></li>
</ul>
<a name="Initialization-of-the-registration-process"></a>
<h2 >Initialization of the registration process<a href="#Initialization-of-the-registration-process" class="wiki-anchor">¶</a></h2>
<p>The initialization of the registration process is triggered by the publisher by sending nomenclatural act data to the registration system via HTTP POST request:</p>
<p>Upon being authenticated the publisher can send the data of the nomenclatural act (Name, Types, Reference ) to a web service endpoint ( ==> <a class="issue tracker-5 status-1 priority-13 priority-high13 parent" title="feature request: registration submission endpoint implemented (New)" href="/redmine/issues/8086">#8086</a>). The model of the data is currently being developed ==> <a class="issue tracker-6 status-1 priority-10 priority-lowest child" title="task: Decide on a data schema to use for submitting nomenclatural acts to the cdm web service (New)" href="/redmine/issues/8085">#8085</a>. For an brief overview on the required data and its granularity, please see the paragraph <strong>Data scope and granularity</strong> below </p>
<ul>
<li>web service URLs:
<ul>
<li>HTTP-POST: <a href="http://api.phycobank.org/phycobank/registration/">http://api.phycobank.org/phycobank/registration/</a></li>
<li>HTTP-PUT: <a href="http://api.phycobank.org/phycobank/registration/%7BphycobankID-urlencoded%7D">http://api.phycobank.org/phycobank/registration/{phycobankID-urlencoded}</a> </li>
</ul></li>
</ul>
<p>As response to the submission the publisher will receive a response object (==> <a class="issue tracker-5 status-1 priority-13 priority-high13 parent" title="feature request: registration submission endpoint implemented (New)" href="/redmine/issues/8086">#8086</a>) which can contain:</p>
<ul>
<li>An HTTP error code (400) with a detailed error message in case the submitted data was causing a problem in the Phycobank system.</li>
<li>The persistent identifier (<a href="http://phycobank.org/%7Binteger%7D">http://phycobank.org/{integer}</a>) for the nomenclatural act. The identifier and according registration is not made public at this point.</li>
<li>The current status of the registration. Initially this is <code>PREPARATION</code></li>
</ul>
<a name="Data-scope-and-granularity"></a>
<h2 >Data scope and granularity<a href="#Data-scope-and-granularity" class="wiki-anchor">¶</a></h2>
<p><em>(For a detailed discussion on this topic please see <a class="issue tracker-6 status-1 priority-10 priority-lowest child" title="task: Decide on a data schema to use for submitting nomenclatural acts to the cdm web service (New)" href="/redmine/issues/8085">#8085</a>)</em></p>
<p>Pyhcobank is a registration for nomenclatural acts. There are two general types of acts to be distinguished:</p>
<ol>
<li>New name + one or more typifications (The new name is the typified name in this case)</li>
<li>One or more typification for an name which has previously been published in an other publication.</li>
</ol>
<p>(Required fields are marked with an asterisk <code>*</code> in the below listings)</p>
<a name="Name"></a>
<h3 >Name<a href="#Name" class="wiki-anchor">¶</a></h3>
<p>A name can have different roles in a nomenclatual act:</p>
<ol>
<li>it is the name being newly published</li>
<li>it is the name for which a typification is published, in this case the name is the <em>typified name</em> (specimen types and name types)</li>
<li>it is used in a typification as type for another name, in this case the name is the type name (name types). </li>
<li>it related to a name used in the cases 1) to 3) as basionym, replaced synonym, validated name or orthographcally corrected name.</li>
</ol>
<ul>
<li><code>genusOrUninomial*</code>:</li>
<li><code>specificEpithet*</code>:</li>
<li><code>rank*</code>: </li>
<li><code>nameType*</code>: (="ICNAFP"), </li>
<li><code>nomenclaturalReference*</code>: </li>
<li><code>citationDetail*</code>:<br></li>
<li><code>nameRelationships</code>: (relations to other name which are basionym, replaced synonym, validated name or orthographcally corrected name.) </li>
</ul>
<a name="Typifications"></a>
<h3 >Typifications<a href="#Typifications" class="wiki-anchor">¶</a></h3>
<a name="Specimen-types"></a>
<h4 >Specimen types<a href="#Specimen-types" class="wiki-anchor">¶</a></h4>
<ul>
<li><code>summary text*</code>: e.g.
<ul>
<li><em>C Ghana 141/1961. “Southwest Ghana. Fresh water (a small stream in bamboo thicket between the villages Agona and Nsuaem, Loc. No. 12). 9.III.1961.”</em></li>
<li><em>NMW C90.12.179 “River Chigara, Sierra Leone”</em></li>
</ul></li>
<li><code>type status*</code>: (holotype, lectotype, ...)</li>
<li><code>kind of unit*</code>: (="Specimen")</li>
<li><code>record basis*</code>: (="PreservedSpecimen")</li>
<li><code>collection code*</code> : Index Herbariorum Code (C, BRM, B, BM or BP etc.)</li>
<li><code>accession number*</code>: e.g. C90.12.179</li>
<li><code>typified name*</code>: (a reference to the typified name) </li>
</ul>
<a name="Name-types"></a>
<h4 >Name types<a href="#Name-types" class="wiki-anchor">¶</a></h4>
<ul>
<li><code>type status*</code>: (e.g. lectotype, original designation, ...)</li>
<li><code>typified name*</code>: (a reference to the typified name) </li>
<li><code>conserved type</code>: [true|false]</li>
<li><code>rejected type</code>: [true|false]</li>
<li><code>not designated type</code>: [true|false]</li>
<li><code>type name*</code>: (a reference to the typified name)</li>
<li><code>citation detail*</code>: </li>
</ul>
<a name="Receiving-messages-from-Phycobank-during-the-edit-and-curation-process"></a>
<h2 >Receiving messages from Phycobank during the edit and curation process<a href="#Receiving-messages-from-Phycobank-during-the-edit-and-curation-process" class="wiki-anchor">¶</a></h2>
<p>The submitted registration record will undergo a manual curation process which may result in a notifications on the registration record. Notifications may report invalidity of the submitted data and thus may be requests for improving data, fixing problems in the submitted nomenclatural act. </p>
<p><del>Prospective service endpoint (<a class="issue tracker-5 status-6 priority-10 priority-lowest closed" title="feature request: Registration message controller implemented (Rejected)" href="/redmine/issues/7270">#7270</a>):</del> rejected, see <a class="issue tracker-6 status-5 priority-10 priority-lowest closed" title="task: Discuss new solution to establish the communication between submitter and curator (Closed)" href="/redmine/issues/7935">#7935</a></p>
<ul>
<li><del><a href="http://api.phycobank.org/phycobank/registration/%7BphycobankID-urlencoded%7D/messages">http://api.phycobank.org/phycobank/registration/{phycobankID-urlencoded}/messages</a></del></li>
<li>Response content type: json</li>
<li>Response content: A list of all messages associated with the registration record sorted by time in ascending order.</li>
<li>authorization required</li>
</ul>
<p>For a new concept see <a class="issue tracker-5 status-6 priority-11 priority-default closed" title="feature request: Feedback mechanism from curator to publisher and author team (Rejected)" href="/redmine/issues/8103">#8103</a></p>
<a name="Requesting-for-the-status-of-a-registration-record"></a>
<h2 >Requesting for the status of a registration record<a href="#Requesting-for-the-status-of-a-registration-record" class="wiki-anchor">¶</a></h2>
<ul>
<li>see <a class="issue tracker-5 status-5 priority-10 priority-lowest closed" title="feature request: Registration not found, Portal handling registrations in preparation (Closed)" href="/redmine/issues/7927">#7927</a> (commit:ebbad31)</li>
<li>HTTP-GET: <a href="http://api.phycobank.org/phycobank/registration/identifier/%7BphycobankID-urlencoded%7D/status.json">http://api.phycobank.org/phycobank/registration/identifier/{phycobankID-urlencoded}/status.json</a></li>
<li>NO authorization required</li>
</ul>
<p><strong>TODO</strong> Can we get rid of the <code>identifier/</code> in the service URL? We could allow for {uuid} and {phycobankID-urlencoded} in the same place.</p>
<p><strong>response data model</strong></p>
<ul>
<li>The webservice responds with the current status which is one of:
<ul>
<li>CURATION</li>
<li>PREPARATION</li>
<li>PUBLISHED</li>
<li>READY</li>
<li>REJECTED</li>
</ul></li>
</ul>
<p>response model ( ==> <a class="issue tracker-6 status-1 priority-13 priority-high13" title="task: improve response model of registration/identifier/{registrationID}/status.json web service (New)" href="/redmine/issues/8087">#8087</a>):</p>
<pre><code class="json syntaxhl"><span class="p">{</span><span class="w">
</span><span class="nl">"registrationId"</span><span class="w"> </span><span class="p">:</span><span class="w"> </span><span class="s2">"{Registration.identifier}"</span><span class="w">
</span><span class="nl">"status"</span><span class="p">:</span><span class="w"> </span><span class="s2">"{Registration.status}"</span><span class="w">
</span><span class="p">}</span><span class="w">
</span></code></pre>
<a name="Publishing-a-registration-identifier"></a>
<h2 >Publishing a registration identifier<a href="#Publishing-a-registration-identifier" class="wiki-anchor">¶</a></h2>
<p>In order to publish the registration of the nomenclatural act the publisher needs to submit the <strong>publication date</strong>, <strong>DOI</strong> and the <strong>pages detail</strong> to Phycobank.</p>
<p>Once all this information is successfully submitted the registration record can potentially change it's status to 'PUBLISHED'. This will immediately happen if the status is 'READY'. It is not guaranteed that the curation process is finished when publishing details are received, in these cases the registration becomes only public once the curator sets the registration status to 'READY'. The persistent Phycobank identifier will only be resolvable once the registration is in state 'PUBLISHED'. Therefore the publisher could consider to postpone the publication of the article until the registration record in the registration is on state 'READY', otherwise the publication would contain a unresolvable identifier.</p>
<p>HTTP-PUT: <a href="http://api.phycobank.org/phycobank/registration/%7BphycobankID-urlencoded%7D">http://api.phycobank.org/phycobank/registration/{phycobankID-urlencoded}</a></p>
<p>Request data which triggers a registration which is READ to change the status to PUBLISHED:</p>
<ul>
<li><strong>publicationDate</strong> : the ISO 8601 date (JJJJ-MM-TT) of the actual publication of the article.</li>
<li><strong>pages</strong> : detail information on the pages covering the published article</li>
<li><strong>doi</strong></li>
</ul>
<a name="Workflow-as-sequence-diagram"></a>
<h2 >Workflow as sequence diagram<a href="#Workflow-as-sequence-diagram" class="wiki-anchor">¶</a></h2>
<p><img src="/redmine/attachments/download/1674/submission%20and%20publication%20with%20curation.png" alt="" /></p>
<a name="Teleconference-on-July-7th-2019"></a>
<h2 >Teleconference on July 7th 2019<a href="#Teleconference-on-July-7th-2019" class="wiki-anchor">¶</a></h2>
<p>Attendees: Andreas Kohlbecker, Teodor Gregoriev and Plamen Pankov from Pensoft Publishers</p>
<p><strong>Data granularity at Pensoft</strong></p>
<p>The data on the nomenclatural acts if available in basically two different granularities. The granularity depends on the workflow in which the journal is processed at Pensoft. </p>
<ul>
<li>Zookeys, Mycokeys, (Phytokeys? ,) ... , have rather low granularity (-> taxon name + status) example: <a href="https://mycokeys.pensoft.net/article/35682/download/xml/">https://mycokeys.pensoft.net/article/35682/download/xml/</a></li>
<li>Biodiversity Journal BDJ has higher granularity (details on typification, etc ...) You can check an example of a paper (although is on Dipter) with new species description: <a href="https://bdj.pensoft.net/article/29553/download/xml/:">https://bdj.pensoft.net/article/29553/download/xml/:</a></li>
</ul>
<p>Excerpt from the BDJ Example: </p>
<pre><code class="xml syntaxhl"><span class="nt"><tp:treatment-sec</span> <span class="na">sec-type=</span><span class="s">"materials"</span><span class="nt">><title></span>Materials<span class="nt"></title><list</span> <span class="na">list-type=</span><span class="s">"alpha-lower"</span> <span class="na">list-content=</span><span class="s">"occurrences"</span><span class="nt">><list-item><p><bold></span>Type status:<span class="nt"></bold><named-content</span> <span class="na">content-type=</span><span class="s">"dwc:typeStatus"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">></span>Holotype<span class="nt"></named-content></span>. <span class="nt"><bold></span>Occurrence:<span class="nt"></bold></span> occurrenceDetails: <span class="nt"><named-content</span> <span class="na">content-type=</span><span class="s">"dwc:occurrenceDetails"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">><ext-link</span> <span class="na">ext-link-type=</span><span class="s">"uri"</span> <span class="na">xlink:href=</span><span class="s">"http://janzen.sas.upenn.edu"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">></span>http://janzen.sas.upenn.edu<span class="nt"></ext-link></named-content></span>; catalogNumber: <span class="nt"><named-content</span> <span class="na">content-type=</span><span class="s">"dwc:catalogNumber"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">></span>DHJPAR0007297<span class="nt"></named-content></span>; recordedBy: <span class="nt"><named-content</span> <span class="na">content-type=</span><span class="s">"dwc:recordedBy"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">></span>D.H. Janzen, W. Hallwachs, <span class="err">&</span> Ruth Franco<span class="nt"></named-content></span>; individualID: <span class="nt"><named-content</span> <span class="na">content-type=</span><span class="s">"dwc:individualID"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">></span>DHJPAR0007297<span class="nt"></named-content></span>; individualCount: <span class="nt"><named-content</span> <span class="na">content-type=</span><span class="s">"dwc:individualCount"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">></span>1<span class="nt"></named-content></span>; sex: <span class="nt"><named-content</span> <span class="na">content-type=</span><span class="s">"dwc:sex"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">></span>male<span class="nt"></named-content></span>; lifeStage: <span class="nt"><named-content</span> <span class="na">content-type=</span><span class="s">"dwc:lifeStage"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">></span>adult<span class="nt"></named-content></span>; preparations: <span class="nt"><named-content</span> <span class="na">content-type=</span><span class="s">"dwc:preparations"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">></span>pinned<span class="nt"></named-content></span>; otherCatalogNumbers: <span class="nt"><named-content</span> <span class="na">content-type=</span><span class="s">"dwc:otherCatalogNumbers"</span> <span class="na">xlink:type=</span><span class="s">"simple"</span><span class="nt">></span>ASTAT069-06 ,04-SRNP-13432, BOLD:ABZ0529<span class="nt"></named-content></span>
</code></pre>
<p>All XMLs and the respective data can be fetched from here: <a href="http://arphahub.com/about/OAI-PMH">http://arphahub.com/about/OAI-PMH</a></p>
<p><strong>Identifier workflow with Zoobank:</strong></p>
<p>Zoobank uses persitent ID in the form of <code>http://www.zoobank.org/NomenclaturalActs/{uuid}</code><br>
Pensoft issues the uuid to be used in the Zoobank identifier and submits the uuid to the registration. </p>
<p><strong>Workflow proposal for interaction of Pensoft with PhycoBank:</strong></p>
<p>Pensoft uses placeholders in the journal data which can be filled with the PhycoBank ID once submitted to the publisher.</p>
<p><strong>1 step registration process:</strong> </p>
<ol>
<li>Pensoft sends all data on the nomenclatural act to PhycoBank together with the scheduled publication date. </li>
<li>PhycoBank returns the PhycoBank identifier</li>
<li>The placeholder in the article is replaced with the PhycoBank ID</li>
<li>PhycoBank sets the Registration status to PUBLISHED by the day of the planned publication date.</li>
</ol>
<p><strong>2 step registration process (optional and under discussion)</strong></p>
<p>This process includes a feedback mechanism from PhycoBank to Pensoft by which the registration can notify the publisher on severe problems in the nomencaltural act. Generally the publication date as planned by Pensoft is 5 days in the future from the day when the nomenclatural act is submitted to PhycoBank. The curation of the registration system theoretically has 4 days to review the submission and to give feedack to the publisher on potential problems in the nomenclatural act. In case of severe problems Pensoft could consider postponing the publication and asking the authors for fixing the problem. </p>
<p><strong>Further steps:</strong></p>
<ul>
<li>PhycoBank will provide user credentials for Pensoft to test the manual data entry as submitter into the PhycoBank registration system. <strong>DONE</strong></li>
<li>Pensoft (Teodor G.) will discuss with the technical staff possibilities of using feedback from the registration system to verify the nomenclatural acts to be published. Submission of a invalid name or typification will result in a warning issued by PhycoBank. This warning could be used to postpone the publication and to ask the authors for correction of the invalid data.</li>
</ul>
<a name="Open-Questions"></a>
<h2 >Open Questions<a href="#Open-Questions" class="wiki-anchor">¶</a></h2>
<ul>
<li>How to deal with new related names? Create blocking registrations?
<ul>
<li>does the publisher need to deal with blocking registrations explicitely or is this been managed behind the scenes for him?</li>
</ul></li>
<li>Discuss: If the object is Multimedia or a strain -> no automatic submission (because this is a different workflow for >5% of the types?</li>
<li>How is data exchanged between Pensoft and <a href="http://www.mycobank.org" class="external">Mycobank</a>?</li>
<li>What is the level of granularity at which Pensoft can deliver data?</li>
</ul>
<hr>
<p>The UML sequence diagram of the workflow is located in the PhycoBank github repository: <a href="https://github.com/cybertaxonomy/PhycoBank/raw/master/digital%20publisher%20workflow%20-%20webservices.xmi" class="external">digital publisher workflow - webservices.xmi</a></p>
</p>
task #6506 (New): Check if a genus has been used before in botany and zoologyhttps://dev.e-taxonomy.eu/redmine/issues/65062017-03-14T11:50:51ZAndreas Kohlbecker
<p>This check will be based in phycobank internal data as well on data available through the Algea names index</p>
<ul>
<li>Gattung in Botanik schon vorhanden NCU ING: STOP-Zeichen</li>
<li>Gattung in Zoologie schon vorhanden: WARN-Zeichen</li>
</ul>
task #6505 (New): Check if type names have never been used as type name beforehttps://dev.e-taxonomy.eu/redmine/issues/65052017-03-14T11:43:46ZAndreas Kohlbecker
<p>This rule needs to be taken into account when a name type is about to be registered for a genus.</p>
<p>The check is performed only on base of the data available internally in phycobank.</p>
task #6168 (Closed): Full registration workflow modelhttps://dev.e-taxonomy.eu/redmine/issues/61682016-10-27T09:02:39ZAndreas Kohlbecker
<p>Model the full registration workflow.</p>
<ul>
<li>An excellent BPMN Documentation is found at: <a href="https://camunda.org/bpmn/reference/">https://camunda.org/bpmn/reference/</a></li>
<li>Camunda also offers a excellent free BPMN editor: <a href="https://camunda.org/download/modeler/">https://camunda.org/download/modeler/</a></li>
</ul>
<p>While being processed in the workflow a registration record can have one of multiple states:</p>
<ul>
<li><strong>preparation</strong>: A new record which is being edited by the Author<br></li>
<li><strong>curation</strong>: A record ready for the curator to be validated.</li>
<li><strong>ready</strong>: The record has passed the validation by the curator and is ready for publication. </li>
<li><strong>published</strong>: The name or typification has finally been published. This state will either be set manually or automatically by the system once the state is <em>ready</em> and when the <code>datePublished</code> and <code>pages</code> of the related Reference is set. For new publications (<code>datePublished</code> >= 2000-01-01) the doi should also be mandatory.</li>
<li><strong>rejected</strong>: The registration has been rejected, the process is aborted and the record is preserved. </li>
</ul>
<hr>
<p>The BPMN file of the workflow is located in the PhycoBank github repository: <a href="https://github.com/cybertaxonomy/PhycoBank/raw/master/AlgenRegistrierungsWorkflow.bpmn" class="external">AlgenRegistrierungsWorkflow.bpmn</a></p>
task #6167 (In Progress): Strategy to avoid locking of names https://dev.e-taxonomy.eu/redmine/issues/61672016-10-26T18:55:26ZAndreas Kohlbecker
<p>Es steht zu befürchten dass Autoren sich Namen dadurch reservieren (locken), dass diese in der Registry als '<em>prospective registration</em>' angelegt werden. Wie kann dies vermieden werden?</p>
<p>Mögliche Strategien:</p>
<ol>
<li>Noch nicht publizierte Namen müssen nach einer gewissen Zeit publiziert oder bestätigt werden, sonst werden sie wieder frei gegeben und können von anderen Autoren verwendet werden. </li>
<li>Namen können nur durch Publisher registriert werden. Siehe ZooKeys 550: 233-246 (2016)</li>
</ol>
task #6014 (New): Use cdmlib validation framework for algae nameshttps://dev.e-taxonomy.eu/redmine/issues/60142016-07-25T13:11:58ZAndreas Kohlbecker
<p>Das Validierungsframework des CDM soll in der AlgenRegistrierung für die Validierung der Algennamen bezüglich der Regeln des ICN verwendet werden.</p>
<p>Allerdings wären, um es für Algen nutzbar zu machen, auch die zahlreichen Sonderregelungen für Algennamen zu bedenken.<br>
Für Pflanzen müssen die meisten Regeln auch noch implementiert werden. Bisher ist das nur für einige Grundregeln passiert, prototypisch.</p>
task #6013 (Closed): Abgleich von Algennamen mit externen Quellenhttps://dev.e-taxonomy.eu/redmine/issues/60132016-07-25T12:33:21ZAndreas Kohlbecker
<p>für die Registrierung von Algennamen haben wir im Antrag angekündigt, Daten mit anderen Datenquellen abzugleichen.</p>
<p>In Blatt 1 des Excel-Blattes habe ich die entsprechenden Datenbanken eingetragen, die sich mit unseren Community-Standards beschäftigen, besonders nomenklatorische Autoren, Index Herbariorum-Codes, Journals, Monographien und Sammler.</p>
<p>In Blatt 2 des Excel-Blattes habe ich die entsprechenden Namens- und Taxondatenbanken eingetragen, jeweils mit Beispiel-Eintrag und Notizen u.a. zu Ids.</p>
<p>siehe <a class="attachment" href="https://dev.e-taxonomy.eu/redmine/attachments/1043">ListeExterneInformation.xls</a></p>
<p>Es sind jeweils Quellen, die für die Registrierungsbelange standardisierte und/oder evaluierte Information bereitstellen könnten. Von einer Eingabehilfe auf Seiten des EDITors über Hinterlegung von Ids und Source des entsprechenden Eintrags in EDIT, bis zum Feedback nicht vorhandener Standardeinträge bei Fremddatenbanken ist schon Verschiedenes andiskutiert worden. Das Ganze dient zunächst der Übersicht, bevor wir in konkretere Planungen einsteigen.</p>