commonmeta-ruby 3.3.18 → 3.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1c4fb0fccfd81d27f198f9cb4f4d56dace1a0ea509f9dfa48603e6b09d5058cf
-  data.tar.gz: d50b7df6d786722b3d86a61da19c1c3083cf2df55c46d9b70393d67532802e43
+  metadata.gz: 75ab77371ac7823493a9e182a81284ae858bc10ee4d2a1df6dd598518024d645
+  data.tar.gz: 696bccaa9835c5b5f7eefc666051fae1d01b608a4e94286b54630053324779b3
 SHA512:
-  metadata.gz: d4b8a03b506d1b14895fdf0f41a66cb45d674f15f0d022826f335048213533d73f32e8394c7f40df5935d7d56670f104b76a1042ed313c88e08ee0a38e1cd89c
-  data.tar.gz: 9af2e1d27abdc064550b95ce544394c72cf319dde10f1e2e33001ee6d61ba57d4554573772059c78a36e7235efd894549225f5090f8e11dcb8e31299701966f0
+  metadata.gz: 6f21095312741ed18d18285ca29c836e1dc528dad317ce501beed5413407ce5d4436660298d9b593eda126e6814b45e0154bd10ec7c8f6e2c4f61794c7e097e7
+  data.tar.gz: 7887477aee2ae90f7a8c271be662ae35bf72c82b69df4afcf41e74ded776c8a96bfbc5af4d04839400cdf57151467b69451e5c5d740ea487b194f2b00bb42984

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    commonmeta-ruby (3.3.18)
+    commonmeta-ruby (3.4.0)
       activesupport (>= 4.2.5, < 8.0)
       addressable (~> 2.8.1, < 2.8.2)
       base32-url (>= 0.7.0, < 1)
@@ -27,7 +27,7 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (7.0.6)
+    activesupport (7.0.7.2)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -37,6 +37,8 @@ GEM
     ast (2.4.2)
     base32-url (0.7.0)
       uuidtools (~> 2.1, >= 2.1.5)
+    base64 (0.1.1)
+    bcp47_spec (0.2.1)
     bibtex-ruby (6.0.0)
       latex-decode (~> 0.0)
     builder (3.2.4)
@@ -60,11 +62,11 @@ GEM
     docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
-    ebnf (2.3.5)
+    ebnf (2.4.0)
       htmlentities (~> 4.3)
-      rdf (~> 3.2)
+      rdf (~> 3.3)
       scanf (~> 1.0)
-      sxp (~> 1.2)
+      sxp (~> 1.3)
       unicode-types (~> 1.8)
     edtf (3.1.1)
       activesupport (>= 3.0, < 8.0)
@@ -92,16 +94,16 @@ GEM
     iniparser (1.0.1)
     json (2.6.3)
     json-canonicalization (0.3.2)
-    json-ld (3.2.5)
+    json-ld (3.3.0)
       htmlentities (~> 4.3)
       json-canonicalization (~> 0.3, >= 0.3.2)
       link_header (~> 0.0, >= 0.0.8)
       multi_json (~> 1.15)
       rack (>= 2.2, < 4)
-      rdf (~> 3.2, >= 3.2.10)
-    json-ld-preloaded (3.2.2)
-      json-ld (~> 3.2)
-      rdf (~> 3.2)
+      rdf (~> 3.3)
+    json-ld-preloaded (3.3.0)
+      json-ld (~> 3.3)
+      rdf (~> 3.3)
     json_schemer (1.0.3)
       hana (~> 1.3)
       regexp_parser (~> 2.0)
@@ -121,12 +123,12 @@ GEM
       crass (~> 1.0.2)
       nokogiri (>= 1.12.0)
     matrix (0.4.2)
-    minitest (5.19.0)
+    minitest (5.20.0)
     multi_json (1.15.0)
     namae (1.1.1)
-    nokogiri (1.15.3-arm64-darwin)
+    nokogiri (1.15.4-arm64-darwin)
       racc (~> 1.4)
-    oj (3.15.1)
+    oj (3.16.1)
     optimist (3.1.0)
     parallel (1.23.0)
     parser (3.2.2.3)
@@ -145,18 +147,19 @@ GEM
       rack (>= 1.3)
     rainbow (3.1.1)
     rake (13.0.6)
-    rdf (3.2.11)
+    rdf (3.3.0)
+      bcp47_spec (~> 0.2)
       link_header (~> 0.0, >= 0.0.8)
-    rdf-rdfxml (3.2.2)
-      builder (~> 3.2)
+    rdf-rdfxml (3.3.0)
+      builder (~> 3.2, >= 3.2.4)
       htmlentities (~> 4.3)
-      rdf (~> 3.2)
-      rdf-xsd (~> 3.2)
-    rdf-turtle (3.2.1)
-      ebnf (~> 2.3)
-      rdf (~> 3.2)
-    rdf-xsd (3.2.1)
-      rdf (~> 3.2)
+      rdf (~> 3.3)
+      rdf-xsd (~> 3.3)
+    rdf-turtle (3.3.0)
+      ebnf (~> 2.4)
+      rdf (~> 3.3)
+    rdf-xsd (3.3.0)
+      rdf (~> 3.3)
       rexml (~> 3.2)
     regexp_parser (2.8.1)
     rexml (3.2.6)
@@ -176,7 +179,8 @@ GEM
     rspec-xsd (0.1.0)
       nokogiri (~> 1.6)
       rspec (~> 3)
-    rubocop (1.55.1)
+    rubocop (1.56.2)
+      base64 (~> 0.1.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -193,12 +197,12 @@ GEM
       rubocop (~> 1.41)
     rubocop-factory_bot (2.23.1)
       rubocop (~> 1.33)
-    rubocop-performance (1.18.0)
+    rubocop-performance (1.19.0)
       rubocop (>= 1.7.0, < 2.0)
       rubocop-ast (>= 0.4.0)
     rubocop-rake (0.6.0)
       rubocop (~> 1.0)
-    rubocop-rspec (2.23.0)
+    rubocop-rspec (2.23.2)
       rubocop (~> 1.33)
       rubocop-capybara (~> 2.17)
       rubocop-factory_bot (~> 2.22)
@@ -213,9 +217,9 @@ GEM
     simplecov_json_formatter (0.1.4)
     simpleidn (0.2.1)
       unf (~> 0.1.4)
-    sxp (1.2.4)
+    sxp (1.3.0)
       matrix (~> 0.4)
-      rdf (~> 3.2)
+      rdf (~> 3.3)
     textutils (1.4.0)
       activesupport
       logutils (>= 0.6.1)
@@ -231,7 +235,7 @@ GEM
     unicode-types (1.8.0)
     uuidtools (2.2.0)
     vcr (6.2.0)
-    webmock (3.18.1)
+    webmock (3.19.1)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)

data/lib/commonmeta/crossref_utils.rb

@@ -63,6 +63,7 @@ module Commonmeta
           insert_crossref_issn(xml)
           insert_item_number(xml)
           insert_crossref_access_indicators(xml)
+          insert_crossref_relations(xml)
           insert_doi_data(xml)
           insert_citation_list(xml)
         end
@@ -81,6 +82,7 @@ module Commonmeta
         insert_item_number(xml)
         insert_crossref_abstract(xml)
         insert_crossref_access_indicators(xml)
+        insert_crossref_relations(xml)
         insert_doi_data(xml)
         insert_citation_list(xml)
       end
@@ -197,6 +199,24 @@ module Commonmeta
       end
     end
 
+    def insert_crossref_relations(xml)
+      return xml if related_identifiers.blank?
+
+      xml.program("xmlns" => "http://www.crossref.org/relations.xsd",
+                  "name" => "relations") do
+        related_identifiers.each do |related_identifier|
+          identifier_type = validate_doi(related_identifier["id"]) ? "doi" : "url"
+          id = identifier_type == "doi" ? doi_from_url(related_identifier["id"]) : related_identifier["id"]
+          attributes = {
+            "relation_type" => related_identifier["type"].camelize(:lower),
+            "identifier_type" => identifier_type,
+          }.compact
+
+          xml.intra_work_relation(id, attributes)
+        end
+      end
+    end
+  
     # def insert_dates(xml)
     #   return xml unless Array.wrap(dates).present?
 

data/lib/commonmeta/readers/json_feed_reader.rb

@@ -57,11 +57,12 @@ module Commonmeta
         language = meta.fetch("language", nil) || meta.dig("blog", "language")
         state = id.present? || read_options.present? ? "findable" : "not_found"
         subjects = Array.wrap(meta.dig("blog", "category")).reduce([]) do |sum, subject|
-          sum += name_to_fos(subject)
+          sum += name_to_fos(subject.underscore.humanize)
 
           sum
         end
         references = get_references(meta)
+        related_identifiers = get_related_identifiers(meta)
         alternate_identifiers = [{ "alternateIdentifier" => meta["id"], "alternateIdentifierType" => "UUID" }]
 
         { "id" => id,
@@ -77,6 +78,7 @@ module Commonmeta
           "license" => license,
           "subjects" => subjects.presence,
           "references" => references.presence,
+          "related_identifiers" => related_identifiers.presence,
           "alternate_identifiers" => alternate_identifiers,
           "state" => state }.compact.merge(read_options)
       end
@@ -103,6 +105,22 @@ module Commonmeta
         end
       end
 
+      def get_related_identifiers(meta)
+        # check that relationships resolve
+        Array.wrap(meta["relationships"]).reduce([]) do |sum, relationship|
+          begin
+            if [200, 301, 302].include? HTTP.head(relationship["url"]).status
+              sum << { "id" => relationship["url"], "type" => relationship["type"] }
+            end
+          rescue => error
+            # puts "Error: #{error.message}"
+            # puts "Error: #{reference}"
+          end
+
+          sum
+        end
+      end
+
       def get_json_feed_unregistered
         # get JSON Feed items not registered as DOIs
 

data/lib/commonmeta/schema_utils.rb

@@ -5,7 +5,7 @@ require "pathname"
 
 module Commonmeta
   module SchemaUtils
-    COMMONMETA = File.read(File.expand_path("../../resources/commonmeta_v0.9.2.json",
+    COMMONMETA = File.read(File.expand_path("../../resources/commonmeta_v0.9.3.json",
                                             __dir__))
 
     def json_schema_errors

data/lib/commonmeta/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Commonmeta
-  VERSION = '3.3.18'
+  VERSION = '3.4.0'
 end

data/resources/{commonmeta_v0.9.2.json → commonmeta_v0.9.3.json}

@@ -1,7 +1,7 @@
 {
   "$schema": "http://json-schema.org/draft-07/schema#",
-  "$id": "https://commonmeta.org/commonmeta_v0.9.2.json",
-  "title": "Commonmeta v0.9.2",
+  "$id": "https://commonmeta.org/commonmeta_v0.9.3.json",
+  "title": "Commonmeta v0.9.3",
   "description": "JSON representation of the Commonmeta schema.",
   "additionalProperties": false,
   "definitions": {
@@ -288,6 +288,36 @@
       },
       "uniqueItems": true
     },
+    "related_identifiers": {
+      "description": "Other resolvable persistent unique IDs related to the resource.",
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "id": {
+            "type": "string"
+          },
+          "type": {
+            "type": "string",
+            "enum": [
+              "IsIdenticalTo",
+              "IsNewVersionOf",
+              "IsPreviousVersionOf",
+              "IsPartOf",
+              "HasPart",
+              "IsVariantFormOf",
+              "IsTranslationOf",
+              "IsVersionOf",
+              "IsReviewOf",
+              "IsPreprintOf",
+              "HasPreprint"
+            ]
+          }
+        },
+        "required": ["id", "type"]
+      },
+      "uniqueItems": true
+    },
     "funding_references": {
       "description": "The funding references for the resource.",
       "type": "array",

data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blog_post_with_non-url_id.yml

@@ -23,13 +23,13 @@ http_interactions:
       Cache-Control:
       - public, max-age=0, must-revalidate
       Content-Length:
-      - '2106'
+      - '8527'
       Content-Type:
       - application/json; charset=utf-8
       Date:
-      - Mon, 10 Jul 2023 21:04:54 GMT
+      - Wed, 06 Sep 2023 14:27:24 GMT
       Etag:
-      - '"13pz9o7pqcg1mi"'
+      - '"sk275cf3ap6kl"'
       Server:
       - Vercel
       Strict-Transport-Security:
@@ -39,7 +39,7 @@ http_interactions:
       X-Vercel-Cache:
       - MISS
       X-Vercel-Id:
-      - fra1::iad1::jbp2f-1689023094094-f2a6094c04f1
+      - fra1::iad1::bsggp-1694010443675-85c6731865df
       Connection:
       - close
     body:
@@ -49,18 +49,84 @@ http_interactions:
         before sunset in Tucson. Live image below, showing the glorious Santa Catalina
         mountains (the snow on the upper reaches is more apparent earlier in the day)
         and my dinner preparations (shrimp and veggies on the grill).I''ve decided
-        to start writing here at Quintessence of Dust, after another long hiatus.
-        Here are some of my reasons.1. I like to write, and I have things to say,
-        and I self-identify as an author. For eight years, I have co-organized and
-        taught in...","published_at":1673233380,"updated_at":1680470227,"indexed_at":1689006804,"authors":[{"url":null,"name":"Stephen
-        Matheson"}],"image":null,"tags":["Introduction"],"language":"en","reference":[],"blog_id":"5764g49","blog_name":"Quintessence
-        of Dust","blog":{"id":"5764g49","title":"Quintessence of Dust","description":"<i>Quintessence
-        of Dust</i> explores science, society, and human nature, focusing on genetics,
-        development, evolution, neuroscience, systems biology, and topics related
-        to scientific literacy. I occasionally discuss intelligent design, creationism,
-        science denial, and other political/social influences on scientific literacy.
-        Additional topics: philosophy, baseball, scientific culture, and Shakespeare.
-        My main theme is <b><u>scientific explanation</u></b>.","language":"en","favicon":null,"feed_url":"http://sfmatheson.blogspot.com/feeds/posts/default","home_page_url":"http://sfmatheson.blogspot.com/","user_id":"8498eaf6-8c58-4b58-bc15-27eda292b1aa","created_at":"2023-05-31T14:21:27+00:00","indexed_at":"2023-04-18","feed_format":"application/atom+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Blogger
-        7.00","category":"Social Sciences","prefix":"10.59350","modified_at":"2023-07-05T03:41:45+00:00","version":"https://jsonfeed.org/version/1.1","backlog":true,"current_feed_url":null,"expired":null}}'
-  recorded_at: Mon, 10 Jul 2023 21:04:54 GMT
+        to start writing here at <i>Quintessence of Dust</i>, after another long hiatus.","content_html":"It''s
+        early January 2023, a little before sunset in Tucson. Live image below, showing
+        the glorious Santa Catalina mountains (the snow on the upper reaches is more
+        apparent earlier in the day) and my dinner preparations (shrimp and veggies
+        on the grill).<div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghgBx9BU21qMDFnLxgHmnsl6TQVfb3QCwOXrC1zcXq7WH9gN8E0TcH3pTslRBG6O8mb5gcuF9JVtDlJ2je6dFcfyzKE4OD38-ftr66nBxddo892_NkyuevrrX65ndSbwmXMaLh3F5yiqU1QIj8JtA8FLkKOcHOEVwVafz0rzh7PejbFzp3XT25nQxc/s4032/Jan%207.jpg\"><img
+        height=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghgBx9BU21qMDFnLxgHmnsl6TQVfb3QCwOXrC1zcXq7WH9gN8E0TcH3pTslRBG6O8mb5gcuF9JVtDlJ2je6dFcfyzKE4OD38-ftr66nBxddo892_NkyuevrrX65ndSbwmXMaLh3F5yiqU1QIj8JtA8FLkKOcHOEVwVafz0rzh7PejbFzp3XT25nQxc/s320/Jan%207.jpg\"
+        width=\"240\" /></a></div><br /><div><div>I''ve decided to start writing here
+        at <i>Quintessence of Dust</i>, after another long hiatus. Here are some of
+        my reasons.</div><div><br /></div><div>1. I like to write, and I have things
+        to say, and I self-identify as an author. For eight years, I have co-organized
+        and taught in the <a href=\"https://meetings.cshl.edu/courses.aspx?course=C-WRITE&amp;year=23\"
+        target=\"_blank\">Scientific Writing Retreat at Cold Spring Harbor Laboratory</a>.
+        I''m a writer and I need to write, if only for myself.</div><div><br /></div><div>2.
+        I have an idea for a book, along with some introductory work (but no sample
+        chapters yet) and writing here will help me develop those thoughts. The idea
+        is over twelve years old and has never faded away, which I take to mean that
+        I need to get it out of my system somehow.</div><div><br /></div><div>3. I
+        have other ideas kicking around in my head and most of them are worth writing
+        about. I have one new intellectual passion that is totally worth writing about:
+        <a href=\"https://skyislandalliance.org/the-sky-islands/\" target=\"_blank\">the
+        Sky Islands</a> that nearly surround us here in Tucson.</div><div><br /></div><div>4.
+        I have an exciting new job with great new people at <a href=\"https://plos.org/\"
+        target=\"_blank\">an organization</a> that''s all in for <a href=\"https://plos.org/open-science/\"
+        target=\"_blank\">open science</a>. I recently turned over the tens digit
+        on my age-o-meter. My kids will very soon be all out of college. (One is about
+        to start a postdoc!) All of this led, predictably, to a spasm of reflection
+        on projects and vision. One clear result is that I''m feeling more inspired.<span><a
+        name=\"more\"></a></span></div><div><br /></div><div>5. The demise of Twitter
+        has led to a lot of <a href=\"https://www.theatlantic.com/technology/archive/2022/11/twitter-facebook-social-media-decline/672074/\"
+        target=\"_blank\">useful commentary</a> about the nature of social media.
+        I left Facebook two years ago and all but left Twitter two months ago. I''m
+        on a <a href=\"https://fediscience.org/explore\" target=\"_blank\">good server
+        at Mastodon</a> and I like it; maybe microblogging there can satisfy my desire
+        for conversation and connection. But <a href=\"https://www.theverge.com/23513418/bring-back-personal-blogging\"
+        target=\"_blank\">this recent piece</a> at <i>The Verge</i> by <a href=\"https://moniquejudge.com/\"
+        target=\"_blank\">Monique Judge</a> convinced me that blogging could (again)
+        have a place in the future.</div><div><br /><div>Here''s her summary, emphasis
+        mine:</div><div><blockquote>At the end of the day, we don’t know what is going
+        to happen next with Twitter or any of these platforms. We don’t know what
+        changes <a href=\"https://www.techtarget.com/whatis/definition/Web-30\" target=\"_blank\">Web
+        3.0</a> is going to bring to the internet. We do know that <b>we will all
+        still be here, wanting to share our thoughts, talk about anything and everything,
+        and commune with our people</b>. Personal blogging is the simplest and fastest
+        way to do all of that. </blockquote></div><div>That''s what I want! A place
+        to write, and (if I''m lucky) a place to discuss and \"commune\" with people.
+        That used to happen a lot at <i>Quintessence of Dust</i>.<span></span></div></div></div><div><br
+        /></div><div>Okay, but why here? This blog is over 15 years old and was started
+        when I was a Christian believer. <a href=\"https://sfmatheson.blogspot.com/2007/08/kicking-off-my-blog.html\"
+        target=\"_blank\">Its founding themes</a> were anchored in a desire to help
+        Christians understand and enjoy biology, to help them shake free of misinformation
+        and dishonesty. It has twice languished through long hiatuses and was <a href=\"https://sfmatheson.blogspot.com/p/about.html\"
+        target=\"_blank\">remodeled</a> back in 2017 a few years after I deconverted.
+        Maybe it''s time to start anew? I think not, for many of those same reasons:
+        I''m still a biologist who loves science, still worried about misinformation,
+        and still rooted in the power of scientific explanation. I''m still a bardolator
+        and a Red Sox fan. <a href=\"https://sfmatheson.blogspot.com/p/about.html\">I''m
+        still me</a>, and <i>Quintessence of Dust</i> is still my blog. The new <a
+        href=\"https://sfmatheson.blogspot.com/p/about.html\" target=\"_blank\">About
+        page</a> is slightly remodeled from 2017, and hints at the next post, which
+        will outline some new goals and ongoing projects.</div><div><br /></div><div>A
+        final note on inspiration, from Imani Perry, writing in her newsletter (<a
+        href=\"https://newsletters.theatlantic.com/unsettled-territory/\" target=\"_blank\">Unsettled
+        Territory</a>) at <i>The Atlantic</i>. The piece is \"<a href=\"https://newsletters.theatlantic.com/unsettled-territory/63af3facace609003751bacc/becoming-writer-habit-journalism/\"
+        target=\"_blank\">Writing is a Democratic Art</a>.\" It''s for subscribers
+        only but here is her challenge:</div><div><blockquote>Thinking and writing
+        at a faster pace stretched me and gave me greater confidence. Sometimes I
+        changed my mind about what I’d written a day later. But that was okay; a newsletter
+        is a moment in time. Writing it each week gave me a lovely rhythm in what
+        has otherwise been a difficult and disorienting season in history. Feeling
+        stuck can get you stuck. But writing can, and should, inspire deeds.</blockquote></div>","published_at":1673233380,"updated_at":1680470227,"indexed_at":1689006804,"authors":[{"url":null,"name":"Stephen
+        Matheson"}],"image":"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghgBx9BU21qMDFnLxgHmnsl6TQVfb3QCwOXrC1zcXq7WH9gN8E0TcH3pTslRBG6O8mb5gcuF9JVtDlJ2je6dFcfyzKE4OD38-ftr66nBxddo892_NkyuevrrX65ndSbwmXMaLh3F5yiqU1QIj8JtA8FLkKOcHOEVwVafz0rzh7PejbFzp3XT25nQxc/s320/Jan%207.jpg","tags":["Introduction"],"language":"en","reference":[],"relationships":[],"blog_id":"5764g49","blog_name":"Quintessence
+        of Dust","blog_slug":"sfmatheson","blog":{"id":"5764g49","title":"Quintessence
+        of Dust","description":"<i>Quintessence of Dust</i> explores science, society,
+        and human nature, focusing on genetics, development, evolution, neuroscience,
+        systems biology, and topics related to scientific literacy. I occasionally
+        discuss intelligent design, creationism, science denial, and other political/social
+        influences on scientific literacy. Additional topics: philosophy, baseball,
+        scientific culture, and Shakespeare. My main theme is <b><u>scientific explanation</u></b>.","language":"en","favicon":null,"feed_url":"http://sfmatheson.blogspot.com/feeds/posts/default","home_page_url":"http://sfmatheson.blogspot.com","user_id":"656f9875-3304-4056-935b-b29429e14222","created_at":"2023-04-18","feed_format":"application/atom+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Blogger
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 recorded_with: VCR 6.2.0

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       string: '{"id":"f3629c86-06e0-42c0-844a-266b03a91ef1","doi":"https://doi.org/10.59350/37y2z-gre70","url":"https://iphylo.blogspot.com/2023/05/ten-years-and-million-links.html","title":"Ten
         years and a million links","summary":"As trailed on a Twitter thread last
         week I’ve been working on a manuscript describing the efforts to map taxonomic
-        names to their original descriptions in the taxonomic literature. Putting
-        together a manuscript on linking taxonomic names to the primary literature,
-        basically “um, what, exactly, have you been doing all these years?”. TL;DR
-        Across fungi, plants, and animals approx 1.3 million names have been linked
-        to a persistent identifier for a publication.— Roderic Page (@rdmpage) May
-        25,...","published_at":1685553960,"updated_at":1685554180,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
-        Page"}],"image":null,"tags":[],"language":"en","reference":[],"blog_id":"tyfqw20","blog_name":"iPhylo","blog":{"id":"tyfqw20","title":"iPhylo","description":"Rants,
+        names to their original descriptions in the taxonomic literature.","content_html":"<p>As
+        trailed on a Twitter thread last week I’ve been working on a manuscript describing
+        the efforts to map taxonomic names to their original descriptions in the taxonomic
+        literature.</p>\n<blockquote><p>Putting together a manuscript on linking taxonomic
+        names to the primary literature, basically “um, what, exactly, have you been
+        doing all these years?”. TL;DR Across fungi, plants, and animals approx 1.3
+        million names have been linked to a persistent identifier for a publication.</p>—
+        Roderic Page (@rdmpage) <a href=\"https://twitter.com/rdmpage/status/1661714128413573120?ref_src=twsrc%5Etfw\">May
+        25, 2023</a></blockquote> \n<p>The preprint is on bioRxiv <a href=\"https://doi.org/10.1101/2023.05.29.542697\">doi:10.1101/2023.05.29.542697</a></p>\n<blockquote>\n<p>A
+        major gap in the biodiversity knowledge graph is a connection between taxonomic
+        names and the taxonomic literature. While both names and publications often
+        have persistent identifiers (PIDs), such as Life Science Identifiers (LSIDs)
+        or Digital Object Identifiers (DOIs), LSIDs for names are rarely linked to
+        DOIs for publications. This article describes efforts to make those connections
+        across three large taxonomic databases: Index Fungorum, International Plant
+        Names Index (IPNI), and the Index of Organism Names (ION). Over a million
+        names have been matched to DOIs or other persistent identifiers for taxonomic
+        publications. This represents approximately 36% of names for which publication
+        data is available. The mappings between LSIDs and publication PIDs are made
+        available through ChecklistBank. Applications of this mapping are discussed,
+        including a web app to locate the citation of a taxonomic name, and a knowledge
+        graph that uses data on researcher’s ORCID ids to connect taxonomic names
+        and publications to authors of those names.</p>\n</blockquote>\n<p>Much of
+        the work has been linking taxa to names, which still has huge gaps. There
+        are also interesting differences in coverage between plants, animals, and
+        fungi (see preprint for details).</p>\n\n<div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s2276/animals-coverage.png\"><img
+        width=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s320/animals-coverage.png\"
+        /></a></div><div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s2276/fungi-coverage.png\"><img
+        width=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s320/fungi-coverage.png\"
+        /></a></div><div><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s2276/plants-coverage.png\"><img
+        width=\"320\" src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s320/plants-coverage.png\"
+        /></a></div>\n\n\nThere is also a simple app to demonstrate these links, see
+        <a href=\"https://species-cite.herokuapp.com\">https://species-cite.herokuapp.com</a>.\n\n\n\n<blockquote>\n<p>Written
+        with <a href=\"https://stackedit.io/\">StackEdit</a>.</p>\n</blockquote>","published_at":1685553960,"updated_at":1685554180,"indexed_at":1689933917,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s320/animals-coverage.png","tags":[],"language":"en","reference":[],"relationships":[],"blog_id":"tyfqw20","blog_name":"iPhylo","blog_slug":"iphylo","blog":{"id":"tyfqw20","title":"iPhylo","description":"Rants,
         raves (and occasionally considered opinions) on phyloinformatics, taxonomy,
         and biodiversity informatics.  For more ranty and less considered opinions,
         see my <a href=\"https://twitter.com/rdmpage\">Twitter feed</a>.<br>ISSN 2051-8188.
         Written content on this site is licensed under a <a href=\"https://creativecommons.org/licenses/by/4.0/\">Creative
-        Commons Attribution 4.0 International license</a>.","language":"en","favicon":null,"feed_url":"https://iphylo.blogspot.com/feeds/posts/default","home_page_url":"https://iphylo.blogspot.com/","user_id":"8498eaf6-8c58-4b58-bc15-27eda292b1aa","created_at":"2023-05-31T08:03:14+00:00","indexed_at":"2023-02-06","feed_format":"application/atom+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Blogger
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+        Commons Attribution 4.0 International license</a>.","language":"en","favicon":null,"feed_url":"https://iphylo.blogspot.com/feeds/posts/default","home_page_url":"https://iphylo.blogspot.com","user_id":"b98bb1b6-b96b-4e8a-94d3-4285ea715f5b","created_at":"2023-02-06","feed_format":"application/atom+xml","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Blogger
+        7.00","category":"computerAndInformationSciences","prefix":"10.59350","modified_at":"2023-08-31T12:36:33+00:00","version":"https://jsonfeed.org/version/1.1","current_feed_url":null,"status":"active","issn":"2051-8188","backlog":0,"authors":null,"plan":"Team","slug":"iphylo","use_mastodon":true}}'
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