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Add codespell support (config, workflow to detect/not fix) and make it fix few typos #25

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6 changes: 6 additions & 0 deletions .codespellrc
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@@ -0,0 +1,6 @@
[codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = .git*,*.pdf,*.svg,*.css,*.min.*,*-min.*,.codespellrc,static
check-hidden = true
ignore-regex = \b(SPACIN|LOD|UE|Alma Mater)\b
# ignore-words-list =
25 changes: 25 additions & 0 deletions .github/workflows/codespell.yml
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# Codespell configuration is within .codespellrc
---
name: Codespell

on:
push:
branches: [master]
pull_request:
branches: [master]

permissions:
contents: read

jobs:
codespell:
name: Check for spelling errors
runs-on: ubuntu-latest

steps:
- name: Checkout
uses: actions/checkout@v4
- name: Annotate locations with typos
uses: codespell-project/codespell-problem-matcher@v1
- name: Codespell
uses: codespell-project/actions-codespell@v2
6 changes: 3 additions & 3 deletions auth_example.json
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Expand Up @@ -24,7 +24,7 @@
"invalid_captcha": "This message warns of an error with the captcha",
"invalid_form": "This message warns that a form cannot be resubmitted"
},
"accesstokensuccess": "Sucess message displayed after an access token request",
"accesstokensuccess": "Success message displayed after an access token request",
"accesstokenconfirm": {
"success": "Access token confirmation ",
"failure": "Message in case of link expiration"
Expand All @@ -33,10 +33,10 @@
"title": "Email title",
"description": "Email description",
"token" : "Message before the button",
"token_button": "Toke button message",
"token_button": "Token button message",
"ignore": "Ignore message in the case of wrong mail",
"signature": "Signature of the email",
"html_message": "Message displayed in the case HTML email is not supported, the link is concatened to this string"
"html_message": "Message displayed in the case HTML email is not supported, the link is concatenated to this string"
}
}
}
2 changes: 1 addition & 1 deletion html-template/about.html
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Expand Up @@ -94,7 +94,7 @@ <h4 id="board">International Advisory Board for <span class="oc-purple">Open</sp
<li><p><a href="https://twitter.com/lariviev">Vincent Larivière</a> (Canadian Research Chair on the Transformation of Scholarly Communication, University of Montréal)</p></li>
<li><p><a href="https://twitter.com/catmacOA">Catriona MacCallum</a> (Director of Open Science, Hindawi Open Access Publisher)</p></li>
<li><p><a href="https://twitter.com/CameronNeylon">Cameron Neylon</a> (Professor of Research Communications, Centre for Culture and Technology, Curtin University)</p></li>
<li><p><a href="https://educopia.org/katherine-skinner/">Katherine Skinner</a> (Reasearch Lead, Invest in Open)</p></li>
<li><p><a href="https://educopia.org/katherine-skinner/">Katherine Skinner</a> (Research Lead, Invest in Open)</p></li>
<li><p><a href="https://cv.archives-ouvertes.fr/didier-torny">Didier Torny</a> (on behalf of the French Open Science Committee)</p></li>
<li><p><a href="https://twitter.com/LudoWaltman">Ludo Waltman</a> (Professor of Quantitative Science Studies and Deputy Director, Centre for Science and Technology Studies (CWTS), Leiden University) <em>[chair]</em></p></li>
</ul>
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8 changes: 4 additions & 4 deletions html-template/ccc.html
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Expand Up @@ -100,13 +100,13 @@ <h4>Scope</h4>
<li><p><strong>Sequence number</strong>:
along with XPath identifiers, discourse elements are identified with a more human-readable sequence number
(e.g. Section n. <code>1</code>, Paragraph n. <code>3</code>, Table n. <code>2</code>),
indentifying their relative position in the document. CCC stores sequence numbers of discourse elements that include at least one in-text reference.</p> </li>
identifying their relative position in the document. CCC stores sequence numbers of discourse elements that include at least one in-text reference.</p> </li>
<li><p><strong>OCI</strong>: an OCI is a global persistent identifier of citations. It usually appears in the form <code>oci:&lt;citing&gt;-&lt;cited&gt;</code> where <code>citing</code> and <code>cited</code> are locally assigned numerical identifiers of respectively a citing document and a cited document.
In CCC an OCI is assigned to both the general citation - in the same form <code>&lt;citing&gt;-&lt;cited&gt;</code> - and to every occurrence of an in-text reference in the citing document relevant to that citation.
For instance: the article identified as <code>0701</code> in CCC cites the article identified as <code>07090</code>, and two in-text references appear in the citing article referencing the cited article.
The general OCI for the citation will be <code>0701-07090</code>, while the two specific citations instatiated by in-text references will be addressed as <code>0701-07090/1</code> and <code>0701-07090/2</code> respectively.</p> </li>
The general OCI for the citation will be <code>0701-07090</code>, while the two specific citations instantiated by in-text references will be addressed as <code>0701-07090/1</code> and <code>0701-07090/2</code> respectively.</p> </li>
<li><p><strong>InTRePID</strong>: the In-Text Reference Pointer Identifier (InTRePID) is a global unique persistent identifier (PID) of in-text reference pointers.
InTRePID is an extention of OCI that appears in the following form: <code>intrepid:&lt;oci&gt;/&lt;ordinal&gt;-&lt;total&gt;</code>
InTRePID is an extension of OCI that appears in the following form: <code>intrepid:&lt;oci&gt;/&lt;ordinal&gt;-&lt;total&gt;</code>
where <code>&lt;oci&gt;</code> is is the numerical part of the OCI identiying a citation between a citing and cited entity,
<code>&lt;ordinal&gt;</code> is the n<sup>th</sup> occurrence of an in-text reference pointer within the text of the citing entity
relevant to the cited entity addressed in the OCI, and <code>&lt;total&gt;</code> is the total number of in-text reference pointers
Expand Down Expand Up @@ -201,7 +201,7 @@ <h4>An example</h4>
datacite:usesIdentifierScheme datacite:oci ;
literal:hasLiteralValue "oci:0701-0702/2".
</code></pre>
<p><em>The first in-text reference <code>rp/0701</code> appears as <code>"Doe et al. 2020"</code>. It appears in the firt section <code>de/0701</code>, called "Introduction",
<p><em>The first in-text reference <code>rp/0701</code> appears as <code>"Doe et al. 2020"</code>. It appears in the first section <code>de/0701</code>, called "Introduction",
second paragraph <code>de/0702</code>, third sentence <code>de/0703</code> (being section, paragraph and sentence numbers relative to the entire document and not to the parent element).
Both in-text references and the discourse elements are also identified by a XPath.</em></p>
<pre><code># the sentence
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2 changes: 1 addition & 1 deletion html-template/datasets.html
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Expand Up @@ -82,7 +82,7 @@ <h3>Datasets</h3>
<!--You can check the statistics of the <a href="/statistics#indexed_records">OpenCitations datasets coverage throughout the time.</a>--></p>
<ul>
<li>
<p><strong><a href="/index"><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Index</a>.</strong> The Index contain information about the citations themselves, in which the citations, instead of being considered as simple links, are treated as <a href="https://opencitations.hypotheses.org/816">first-class data entities</a> in their own right. The Index do not store metadata about the citing and cited bibliographic entities internally. Rather, these entities are identified in the Index by their unique identifiers, i.e. the <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta Indentifier (OMID), enabling bibliographic information to be retrieved on-the-fly upon request by means of the <a href="/meta/api/v1"><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta API</a>.
<p><strong><a href="/index"><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Index</a>.</strong> The Index contain information about the citations themselves, in which the citations, instead of being considered as simple links, are treated as <a href="https://opencitations.hypotheses.org/816">first-class data entities</a> in their own right. The Index do not store metadata about the citing and cited bibliographic entities internally. Rather, these entities are identified in the Index by their unique identifiers, i.e. the <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta Identifier (OMID), enabling bibliographic information to be retrieved on-the-fly upon request by means of the <a href="/meta/api/v1"><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta API</a>.
</li>
<li><p><strong><a href="/meta"><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta</a>.</strong> OpenCitations Meta stores and delivers bibliographic metadata for all publications involved in the OpenCitations Index.</p></li>
</ul>
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2 changes: 1 addition & 1 deletion html-template/download_legacy.html
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Expand Up @@ -78,7 +78,7 @@ <h3 class="masthead-brand">

<div class="cover left">
<h3>$active.title()</h3>
<p><strong>This page is a legacy page (not linked anymore from the official website) that links all the dumps produced by OpenCitations before October 2023 that are not mantained anymore.</strong></p>
<p><strong>This page is a legacy page (not linked anymore from the official website) that links all the dumps produced by OpenCitations before October 2023 that are not maintained anymore.</strong></p>
<p>This page details of and links to all the data dumps of the <a href="#index"><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Indexes</a>, the <a href="#ccc"><span class="oc-purple">Open</span> Biomedical <span class="oc-blue">Citations</span> in Context Corpus</a> and of the <a href="#occ"><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Corpus (OCC)</a>. They are made available online by means of the support of <a href="http://figshare.com">Figshare</a> and of the <a href="https://archive.org/">Internet Archive</a>.</p>
<p>Each dump of an <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Index is composed by four zip archives. Two of these archives contains the actual data and provenance information of the index in N-Triples, while the other two archives contain the same information in CSV.</p>
<p>Each dump of the <span class="oc-purple">Open</span> Biomedical <span class="oc-blue">Citations</span> in Context Corpus is composed by one single zip artchive containing all the information about actual data and provenance stored in JSON-LD.</p>
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2 changes: 1 addition & 1 deletion html-template/home.html
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Expand Up @@ -85,7 +85,7 @@ <h1 class="cover-heading">

<p><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> is an independent not-for-profit infrastructure organization for open scholarship dedicated to the publication of open bibliographic and citation data by the use of <a href="https://en.wikipedia.org/wiki/Semantic_Web">Semantic Web</a> (<a href="https://en.wikipedia.org/wiki/Linked_data">Linked Data</a>) technologies. It is also engaged in advocacy for open citations, particularly in its role as a key founding member of the <a href="https://i4oc.org">Initiative for Open Citations (I4OC)</a>. For administrative convenience, <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> is managed by the <a href="https://openscholarlymetadata.org">Research Centre for Open Scholarly Metadata</a> at the <a href="https://www.unibo.it/en">University of Bologna</a>.</p>

<p><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> espouses fully the founding principles of Open Science. It complies with the <a href="https://doi.org/10.1038/sdata.2016.18">FAIR data principles</a> by <a href="https://www.force11.org">Force11</a> that data should be <strong>findable</strong>, <strong>accessible</strong>, <strong>interoperable</strong> and <strong>re-usable</strong>, and it complies with the recommendations of <a href="https://i4oc.org">I4OC</a> that citation data in particular should be <strong>structured</strong>, <strong>separable</strong>, and <strong>open</strong>. On the latter topic, <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> has recently published a formal definition of an <a href="https://doi.org/10.6084/m9.figshare.6683855">Open Citation</a>, and has launched a system for globally unique and persistent identifiers (PIDs) for bibliographic citations – <a href="https://doi.org/10.6084/m9.figshare.7127816">Open Citation Identifiers (OCIs)</a>.</p>
<p><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> espouses fully the founding principles of Open Science. It complies with the <a href="https://doi.org/10.1038/sdata.2016.18">FAIR data principles</a> by <a href="https://www.force11.org">Force11</a> that data should be <strong>findable</strong>, <strong>accessible</strong>, <strong>interoperable</strong> and <strong>reusable</strong>, and it complies with the recommendations of <a href="https://i4oc.org">I4OC</a> that citation data in particular should be <strong>structured</strong>, <strong>separable</strong>, and <strong>open</strong>. On the latter topic, <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> has recently published a formal definition of an <a href="https://doi.org/10.6084/m9.figshare.6683855">Open Citation</a>, and has launched a system for globally unique and persistent identifiers (PIDs) for bibliographic citations – <a href="https://doi.org/10.6084/m9.figshare.7127816">Open Citation Identifiers (OCIs)</a>.</p>

<p><span class="oc-purple">Open</span><span class="oc-blue">Citations'</span> involvement in international networks and collaborations, together with the need of identifying and reaching out to new stakeholders to assure <span class="oc-purple">Open</span><span class="oc-blue">Citations'</span> development and sustainability, has made it necessary to define <span class="oc-purple">Open</span><span class="oc-blue">Citations'</span> mission, unique strengths and next developmental steps, summarized in the following publicly available documents: <a href="https://zenodo.org/record/6976670">OpenCitations Mission Statement</a>, <a href="https://zenodo.org/record/6976696">The Uniqueness of OpenCitations</a> and <a href="https://zenodo.org/record/6976691">OpenCitations – Present Status and Future Plans.</a></p>

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4 changes: 2 additions & 2 deletions html-template/meta.html
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Expand Up @@ -80,7 +80,7 @@ <h3 class="masthead-brand">
<h3><span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta</h3>
<p>The <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta database stores and delivers bibliographic metadata for all publications involved in the <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Index.</p>

<p>For each publication, the metadata exposed by <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta includes the publication's <strong>title</strong>, <strong>type</strong>, <strong>venue</strong> (e.g. journal name), <strong>volume</strong> number, <strong>issue</strong> number, <strong>page</strong> numbers, <stong>publication date</strong>, and <strong>identifiers</strong> such as Digital Object Identifiers (DOIs) and PubMed Identifiers (PMIDs). In addition, <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta includes details of the main actors involved in the publication of the document, i.e., the names of the <strong>authors</strong>, <strong>editors</strong>, and <strong>publishers</strong>, each with its own additional metadata and identifier (e.g. ORCID).</p>
<p>For each publication, the metadata exposed by <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta includes the publication's <strong>title</strong>, <strong>type</strong>, <strong>venue</strong> (e.g. journal name), <strong>volume</strong> number, <strong>issue</strong> number, <strong>page</strong> numbers, <strong>publication date</strong>, and <strong>identifiers</strong> such as Digital Object Identifiers (DOIs) and PubMed Identifiers (PMIDs). In addition, <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta includes details of the main actors involved in the publication of the document, i.e., the names of the <strong>authors</strong>, <strong>editors</strong>, and <strong>publishers</strong>, each with its own additional metadata and identifier (e.g. ORCID).</p>

<p>Currently, <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta contains:</p>
<ul>
Expand All @@ -98,7 +98,7 @@ <h4>Entity URLs</h4>

<h4>The <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta Identifier</h4>
<p>Every entity in <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta is assigned persistent internal identifier called <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta Identifier (OMID). The OMID has structure <code>[[entity_type_abbreviation]]/[[supplier_prefix]][[sequential_number]]</code>.
For example, the first journal article ever processed has OMID <code>br/0601</code> (the full URI is <a href="https://w3id.org/oc/meta/br/0601" alt="Link to an examplar entity from OpenCitations Meta">https://w3id.org/oc/meta/br/0601</a>), where <code>br</code> is the abbreviation of bibliographic resource, and <code>060</code> corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta). Finally, <code>1</code> indicates that this is the index's first bibliographic resource ever minted.</p>
For example, the first journal article ever processed has OMID <code>br/0601</code> (the full URI is <a href="https://w3id.org/oc/meta/br/0601" alt="Link to an exemplar entity from OpenCitations Meta">https://w3id.org/oc/meta/br/0601</a>), where <code>br</code> is the abbreviation of bibliographic resource, and <code>060</code> corresponds to the supplier prefix, helpful in recognising at a glance the index it belongs to (i.e., <span class="oc-purple">Open</span><span class="oc-blue">Citations</span> Meta). Finally, <code>1</code> indicates that this is the index's first bibliographic resource ever minted.</p>

<p>The entities subject to deduplication and associated with an OMID are <strong>identifiers</strong> (abbr. <code>id</code>), <strong>agent roles</strong> (i.e., authors, editors, publishers, abbr. <code>ar</code>),
<strong>responsible agents</strong> (i.e., people and organisations, abbr. <code>ra</code>), <strong>resource embodiments</strong> (i.e., pages, abbr. <code>re</code>),
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