commonmeta-ruby 3.3.16 → 3.3.17

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1959fba18a127e97c92b94c7e0e78d42c4538e3bccf6b9e6019035931e19d2f4
-  data.tar.gz: 190a4ddc0e6789c56f6f9a5a97355c8684e103abf121d2dfefdd5c1d816bd2d2
+  metadata.gz: 3d9089eaa55c76c89411f0b252418860d40c498b77ad5e07ff6937d26364fff4
+  data.tar.gz: b251346f6fd8fe1714632587ee46196b00c3c4bb8c4ba7bf0fe6decd54c5a9e3
 SHA512:
-  metadata.gz: d5994587ca3efda69c8f1e4efca204a89db31d9e4b48a4b683e0312e32209c720f3a24506026152dd69d6ee49895919d72ee4d3aea6557da2b972a1fdb94092a
-  data.tar.gz: 56b4e03114cff5155c502f08f953afb3f2ba13c82bdefecfed73b752131b6b718cd21460eaa8d6506b7b50ded9655330e7c040c833a81c5feeb105c489306ab9
+  metadata.gz: 87733ee7cf23b71317df6c8ef7ad2eea099db43a6291a948f93b18220aeff5f3cf72e8ec9a9b0e36b3f243fe7b651d1b7d401341d0cf0524d0a6c3ea0db1bc7f
+  data.tar.gz: 131dbb14b63cca5c62acce085746f0dc13ef99252bd9243a84c0565a5e671e45c613cc12903df297e4c9df8bd0f5a6d69b645d18e622dd895c0d120e0d7b7f46

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    commonmeta-ruby (3.3.16)
+    commonmeta-ruby (3.3.17)
       activesupport (>= 4.2.5, < 8.0)
       addressable (~> 2.8.1, < 2.8.2)
       base32-url (>= 0.7.0, < 1)

data/lib/commonmeta/readers/json_feed_reader.rb

@@ -21,7 +21,7 @@ module Commonmeta
         meta = string.present? ? JSON.parse(string) : {}
 
         url = normalize_url(meta.fetch("url", nil))
-        id = options[:doi] ? normalize_doi(options[:doi]) : normalize_id(meta.fetch("id", nil))
+        id = options[:doi] ? normalize_doi(options[:doi]) : normalize_id(meta.fetch("doi", nil))
         id = url if id.blank? && url.present?
 
         type = "Article"
@@ -34,8 +34,8 @@ module Commonmeta
         publisher = { "name" => meta.dig("blog", "title") }
 
         date = {}
-        date["published"] = get_iso8601_date(meta.dig("date_published")) if meta.dig("date_published").present?
-        date["updated"] = get_iso8601_date(meta.dig("date_modified")) if meta.dig("date_modified").present?
+        date["published"] = get_date_from_unix_timestamp(meta.dig("published_at")) if meta.dig("published_at").present?
+        date["updated"] = get_date_from_unix_timestamp(meta.dig("updated_at")) if meta.dig("updated_at").present?
 
         license = if meta.dig("blog", "license").present?
             hsh_to_spdx("rightsURI" => meta.dig("blog", "license"))
@@ -62,7 +62,7 @@ module Commonmeta
           sum
         end
         references = get_references(meta)
-        alternate_identifiers = [{ "alternateIdentifier" => meta["uuid"], "alternateIdentifierType" => "UUID" }]
+        alternate_identifiers = [{ "alternateIdentifier" => meta["id"], "alternateIdentifierType" => "UUID" }]
 
         { "id" => id,
           "type" => type,
@@ -83,7 +83,7 @@ module Commonmeta
 
       def get_references(meta)
         # check that references resolve
-        Array.wrap(meta["references"]).reduce([]) do |sum, reference|
+        Array.wrap(meta["reference"]).reduce([]) do |sum, reference|
           begin
             if reference["doi"] && validate_doi(reference["doi"])
               response = HTTP.follow
@@ -122,7 +122,6 @@ module Commonmeta
         return { "string" => nil, "state" => "not_found" } unless response.status.success?
 
         posts = JSON.parse(response.body.to_s)
-        puts posts.inspect
         posts.map { |post| post["id"] }.first
       end
 

data/lib/commonmeta/utils.rb

@@ -1094,6 +1094,20 @@ module Commonmeta
       nil
     end
 
+    # parsing of unix timestamps such as 1427846400
+    def get_datetime_from_unix_timestamp(unix_timestamp)
+      strip_milliseconds(DateTime.strptime(unix_timestamp.to_s, '%s').iso8601)
+    rescue StandardError
+      nil
+    end
+
+    # parsing of unix timestamps such as 1427846400
+    def get_date_from_unix_timestamp(unix_timestamp)
+      DateTime.strptime(unix_timestamp.to_s, '%s').strftime('%Y-%m-%d')
+    rescue StandardError
+      nil
+    end
+
     # strip milliseconds if there is a time, as it interferes with edtc parsing
     # keep dates unchanged
     def strip_milliseconds(iso8601_time)

data/lib/commonmeta/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Commonmeta
-  VERSION = '3.3.16'
+  VERSION = '3.3.17'
 end

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

@@ -23,28 +23,28 @@ http_interactions:
       Cache-Control:
       - public, max-age=0, must-revalidate
       Content-Length:
-      - '8562'
+      - '2106'
       Content-Type:
       - application/json; charset=utf-8
       Date:
-      - Sun, 18 Jun 2023 15:23:52 GMT
+      - Mon, 10 Jul 2023 21:04:54 GMT
       Etag:
-      - '"12ofvtx6pm66lo"'
+      - '"13pz9o7pqcg1mi"'
       Server:
       - Vercel
       Strict-Transport-Security:
       - max-age=63072000
       X-Matched-Path:
-      - "/api/posts/[slug]"
+      - "/api/posts/[[...params]]"
       X-Vercel-Cache:
       - MISS
       X-Vercel-Id:
-      - fra1::iad1::v8bjb-1687101832274-be4cfdb8ff78
+      - fra1::iad1::jbp2f-1689023094094-f2a6094c04f1
       Connection:
       - close
     body:
       encoding: UTF-8
-      string: '{"id":"https://doi.org/10.59350/63055-a8604","uuid":"1898d2d7-4d87-4487-96c4-3073cf99e9a5","url":"http://sfmatheson.blogspot.com/2023/01/quintessence-of-dust-2023-restart-why.html","title":"Quintessence
+      string: '{"id":"1898d2d7-4d87-4487-96c4-3073cf99e9a5","doi":"https://doi.org/10.59350/63055-a8604","url":"http://sfmatheson.blogspot.com/2023/01/quintessence-of-dust-2023-restart-why.html","title":"Quintessence
         of Dust 2023 restart: the why","summary":"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)
@@ -52,85 +52,15 @@ http_interactions:
         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...","date_published":"2023-01-09T03:03:00Z","date_modified":"2023-04-02T21:17:07Z","date_indexed":"2023-06-18T13:32:03.284651+00:00","authors":[{"url":null,"name":"Stephen
-        Matheson"}],"image":null,"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 class=\"separator\"
-        style=\"clear: both; text-align: center;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghgBx9BU21qMDFnLxgHmnsl6TQVfb3QCwOXrC1zcXq7WH9gN8E0TcH3pTslRBG6O8mb5gcuF9JVtDlJ2je6dFcfyzKE4OD38-ftr66nBxddo892_NkyuevrrX65ndSbwmXMaLh3F5yiqU1QIj8JtA8FLkKOcHOEVwVafz0rzh7PejbFzp3XT25nQxc/s4032/Jan%207.jpg\"
-        style=\"clear: right; float: right; margin-bottom: 1em; margin-left: 1em;\"><img
-        border=\"0\" data-original-height=\"4032\" data-original-width=\"3024\" 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>&nbsp;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&nbsp;<a href=\"https://fediscience.org/explore\" target=\"_blank\">good
-        server at Mastodon</a>&nbsp;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.&nbsp;</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>","tags":["Introduction"],"language":"en","references":[],"blog_id":"5764g49","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":"2023-06-06T20:22:00+00:00","version":"https://jsonfeed.org/version/1.1","backlog":true,"authors":null}}'
-  recorded_at: Sun, 18 Jun 2023 15:23:52 GMT
-recorded_with: VCR 6.1.0
+        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
+recorded_with: VCR 6.2.0

data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_json_feed_item_metadata/blogger_post.yml

@@ -23,28 +23,28 @@ http_interactions:
       Cache-Control:
       - public, max-age=0, must-revalidate
       Content-Length:
-      - '6686'
+      - '2018'
       Content-Type:
       - application/json; charset=utf-8
       Date:
-      - Sun, 18 Jun 2023 15:23:54 GMT
+      - Mon, 10 Jul 2023 21:04:51 GMT
       Etag:
-      - '"w9llnwc692558"'
+      - '"rlf5k9cygn1ju"'
       Server:
       - Vercel
       Strict-Transport-Security:
       - max-age=63072000
       X-Matched-Path:
-      - "/api/posts/[slug]"
+      - "/api/posts/[[...params]]"
       X-Vercel-Cache:
       - MISS
       X-Vercel-Id:
-      - fra1::iad1::22vn2-1687101834016-bcd59dbcc91c
+      - fra1::iad1::9gxbv-1689023091514-026dffac583b
       Connection:
       - close
     body:
       encoding: UTF-8
-      string: '{"id":"https://doi.org/10.59350/37y2z-gre70","uuid":"f3629c86-06e0-42c0-844a-266b03a91ef1","url":"https://iphylo.blogspot.com/2023/05/ten-years-and-million-links.html","title":"Ten
+      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
@@ -52,52 +52,13 @@ http_interactions:
         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,...","date_published":"2023-05-31T17:26:00Z","date_modified":"2023-05-31T17:29:40Z","date_indexed":"2023-06-16T11:31:55.22232+00:00","authors":[{"url":null,"name":"Roderic
-        Page"}],"image":null,"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
-        class=\"twitter-tweet\"><p lang=\"en\" dir=\"ltr\">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 class=\"separator\" style=\"clear:
-        both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdWsSQhqi1DErXMIHm28g37-fiALNIsI5eQZmvoX_Fe03ZSwtKHbYt-LCsCCAUop0AGcwy_w7NpIjylVH1hNrM9oW-6j9e6tHASha49TTqFvDg2_tEx3r74RRFsjUo4M_Qat8NmKaZSChOt2hI3LsMjTVLrEVirEckU-9Ei7ug-7OHQlR4LA/s2276/animals-coverage.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"320\" data-original-height=\"2276\" data-original-width=\"2276\"
-        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
-        class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s2276/fungi-coverage.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"320\" data-original-height=\"2276\" data-original-width=\"2276\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjdyxlVJ-oyMCNPmHtHWjSxdxMSJvgzdWRGRF6Ad4dk7ab7gGDpuKdKmS9XhROkopw361ylfsTd1ZkwkF6BN0JlWNnVLCKY1AfryCfWKHkgPQM7u-0SELW9j8RlQIflb6ibaV64gwW7oJrEvOGECvR51F8EW8cRg-1usW-GBM5ymObj7zlObQ/s320/fungi-coverage.png\"/></a></div><div
-        class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgf0YBuvNSXWAJTfQ1jk4XSocMzCYHP7t6IPUqhjQ3mftgM_850igWaD2copgNH6Xk6T62xBU641wvwOvXgCCDY3m2xC_gaILXO9RGx8H3Gpy5OOncsLb9smpT2LIgtYOExVBVdDRWqA0AZ8-mQjWL7dL5TiG7MqVu8spT8ACoGOPR_T36hRA/s2276/plants-coverage.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"320\" data-original-height=\"2276\" data-original-width=\"2276\"
-        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>","tags":[],"language":"en","references":[],"blog_id":"tyfqw20","blog":{"id":"tyfqw20","title":"iPhylo","description":"Rants,
+        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,
         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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-      string: '{"id":"https://doi.org/10.59350/ytvy2-59450","uuid":"6179ad80-cc7f-4904-9260-0ecb3c3a90ba","url":"https://www.ideasurg.pub/academic-powerhouse/","title":"How
-        to Build an Academic Powerhouse: Let''s Study Who''s Doing it","summary":"A
-        Data Exploration with Public Data from the Academic Surgical Congress","date_published":"2023-06-03T04:54:30Z","date_modified":null,"date_indexed":"2023-06-16T14:13:56.969774+00:00","authors":[{"url":null,"name":"Tejas
-        S. Sathe, MD"}],"image":null,"content_html":"<p>Students and residents aspiring
-        for a career in academic surgery are looking for training programs that will
-        help jumpstart their careers by exposing them to mentorship and opportunities
-        to conduct research. While the gold standard of academic productivity (for
-        the time being) remains peer-reviewed publications, conference presentations
-        are an important secondary metric. In addition to feeding eventual papers,
-        conference talks allow trainees to practice presentation skills, build their
-        networks, and learn about the work being done at peer institutions and the
-        field more broadly. Residents pursuing professional development are encouraged
-        to apply to and attend conferences, though in the post COVID era the cost
-        of conference attendance and travel are being re-evaluated. Even moreso than
-        publications, conference presentations are typically led by students and residents.
-        For now, academic conference participation can serve as an important albeit
-        limited metric to evaluate an overall institution''s research power &#x2013;
-        especially as it relates to trainees.</p><p>In order to understand how to
-        build a successful research program, we wanted to understand who had already
-        done so. Conceivably, by finding successful examples, we can conduct interviews
-        and focus groups among key stakeholders at these programs to understand what
-        they did, and how these actions can be replicated. We were particularly interested
-        in seeing which programs demonstrated a high number of accepted abstracts
-        and which programs were able to improve their abstract performance from year
-        to year. </p><p>The <a href=\"https://www.academicsurgicalcongress.org/?ref=ideasurg.pub\">Academic
-        Surgical Congress</a> (ASC) is a joint surgical meeting co-hosted by the <a
-        href=\"https://www.aasurg.org/?ref=ideasurg.pub\">Association for Academic
-        Surgery</a> (AAS) and the <a href=\"https://www.susweb.org/?ref=ideasurg.pub\">Society
-        for University Surgeons</a> (SUS) and held annually in February. Anecdotally,
-        it is a popular conference for students and residents to attend. The ASC maintains
-        a public archive of all abstracts dating from 2015-2020. We obtained a machine
-        readable version of this public database through the webmaster (this version
-        of the data spans 2016 to 2023).</p><p>For each abstract, we looked at the
-        year and primary institution at which the work was conducted. In order to
-        intuit the primary institution, we searched the institution block string for
-        the first presence of \"university\", \"hospital\", \"institute\", or \"medical
-        center\" or the first expression to occur before a comma. This method was
-        chosen as institutions&#x2019; names are written variably (Department of Surgery,
-        University Hospital, New York, NY vs. University Hospital, Division of Colorectal
-        Surgery, Department of Surgery, New York, NY). Unfortunately, our code is
-        unable to merge slight variations in the resultant institution name (University
-        of Michigan vs. University of Michigan Ann Arbor). </p><p>In order to do a
-        primary survey of institutional trends in this dataset, we conducted the following
-        analyses. First, we measured the number of abstracts accepted each year from
-        2016 to 2023. Second, we looked at the number of accepted abstracts by institution
-        over the entire study period. Then, we looked at the number of abstract institutions
-        by institution and year to study changes in institutional trends over time.
-        Finally, we did a subset analysis on post-COVID data (2021 to 2023) to look
-        at absolute and per cent year-over-year changes in accepted abstracts to see
-        which institutions were able to significantly increase their abstract performance
-        in one year. </p><h3 id=\"accepted-abstracts-are-increasing-but-down-from-peak\">Accepted
-        Abstracts are increasing but down from peak</h3><p>We plotted the total number
-        of abstracts accepted by year. The number of accepted abstracts increased
-        from 1125 in 2016 to an all-time high of 1742 in 2020 before declining to
-        922 and 848 in 2021 and 2022, respectively. Accepted abstracts have since
-        rebounded to 1469 in 2023, or roughly 84% of the maximum amount. Of note,
-        the 2021 and 2022 meetings were held virtually due to the COVID-19 pandemic.
-        Conversely the 2020 meeting was held immediately prior to the institution
-        of lockdowns and other social distancing policies.</p><figure class=\"kg-card
-        kg-image-card kg-width-wide\"><img src=\"https://www.ideasurg.pub/content/images/2023/06/newplot--1-.png\"
-        class=\"kg-image\" alt loading=\"lazy\" width=\"1400\" height=\"800\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/newplot--1-.png
-        600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/newplot--1-.png
-        1000w, https://www.ideasurg.pub/content/images/2023/06/newplot--1-.png 1400w\"
-        sizes=\"(min-width: 1200px) 1200px\"></figure><h3 id=\"alabama-michigan-lead-abstract-acceptances-during-study-period\">Alabama,
-        Michigan lead abstract acceptances during study period</h3><p>Next, we plotted
-        the total number of accepted abstracts by institution. The graph shows data
-        for the twenty leading institutions. The University of Alabama and the University
-        of Michigan lead in abstract acceptances during the study period (477 and
-        348, respectively). Given an eight year time-range, the top twenty institutions
-        reflect an average annual abstract acceptance ranging from roughly thirteen
-        to 60.</p><figure class=\"kg-card kg-image-card kg-width-wide\"><img src=\"https://www.ideasurg.pub/content/images/2023/06/newplot--2-.png\"
-        class=\"kg-image\" alt loading=\"lazy\" width=\"1400\" height=\"800\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/newplot--2-.png
-        600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/newplot--2-.png
-        1000w, https://www.ideasurg.pub/content/images/2023/06/newplot--2-.png 1400w\"
-        sizes=\"(min-width: 1200px) 1200px\"></figure><p>We also plotted the number
-        of accepted abstracts by year using a separate line plot for each individual.
-        While Michigan has maintained between 30 and 60 abstracts for each year, Alabama
-        went from 6 to 48 abstracts between 2016 and 2017 and has maintained greater
-        than 60 accepted abstracts each year. There is a notable dip in the number
-        of accepted abstracts from 2021 to 2022, consistent with a similar trend in
-        the total yearly acceptance data. </p><figure class=\"kg-card kg-image-card
-        kg-width-wide\"><img src=\"https://www.ideasurg.pub/content/images/2023/06/newplot--8-.png\"
-        class=\"kg-image\" alt loading=\"lazy\" width=\"1400\" height=\"800\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/newplot--8-.png
-        600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/newplot--8-.png
-        1000w, https://www.ideasurg.pub/content/images/2023/06/newplot--8-.png 1400w\"
-        sizes=\"(min-width: 1200px) 1200px\"></figure><p>Overall, there appears to
-        be a general clustering of the other eighteen institutions in the top twenty,
-        a trend seen in both the aggregate and the year-to-year data.</p><h3 id=\"mgh-brigham-lead-absolute-and-per-cent-increase-in-abstracts-in-2023\">MGH,
-        Brigham lead absolute and per cent increase in abstracts in 2023</h3><p>Next,
-        we measured the absolute and percent change between accepted abstracts in
-        consecutive years for the top twenty institutions. We restricted our analysis
-        to 2021, 2022, and 2023. The greatest absolute increases in accepted abstracts
-        came from Massachusetts General Hospital in 2023 (27), Brigham and Women''s
-        Hospital in 2023 (16), and UCLA in 2022 (16). The greatest percentage increases
-        in accepted abstracts came from Brigham and Women''s Hospital in 2023 (800%),
-        Johns Hopkins in 2023 (500%), and Massachusetts General Hospital in 2023 (386%).
-        Of note, Johns Hopkins and Brigham and Women''s Hospital also had the largest
-        absolute and percentage decrease in accepted abstracts in 2022. Interestingly,
-        University of Alabama (+4 in 2022, +3 in 2023) and University of Michigan
-        (+11 in 2023) &#xA0;- which rank at the top in all time and yearly abstracts
-        - experienced less extreme swings during the 2021-2023 time period.</p><figure
-        class=\"kg-card kg-image-card kg-width-wide\"><img src=\"https://www.ideasurg.pub/content/images/2023/06/newplot--7-.png\"
-        class=\"kg-image\" alt loading=\"lazy\" width=\"1400\" height=\"800\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/newplot--7-.png
-        600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/newplot--7-.png
-        1000w, https://www.ideasurg.pub/content/images/2023/06/newplot--7-.png 1400w\"
-        sizes=\"(min-width: 1200px) 1200px\"></figure><figure class=\"kg-card kg-image-card
-        kg-width-wide\"><img src=\"https://www.ideasurg.pub/content/images/2023/06/newplot--4-.png\"
-        class=\"kg-image\" alt loading=\"lazy\" width=\"1400\" height=\"800\" srcset=\"https://www.ideasurg.pub/content/images/size/w600/2023/06/newplot--4-.png
-        600w, https://www.ideasurg.pub/content/images/size/w1000/2023/06/newplot--4-.png
-        1000w, https://www.ideasurg.pub/content/images/2023/06/newplot--4-.png 1400w\"
-        sizes=\"(min-width: 1200px) 1200px\"></figure><h3 id=\"conclusions\">Conclusions</h3><p>In
-        this data exploration, we analyzed abstract acceptance data for the Academic
-        Surgical Congress between 2016 and 2023. We showed that the number of abstracts
-        increased from 2016 to 2020, dipped in 2021 and 2022, and is recovering in
-        2023 - likely reflecting the variability forced by COVID19 and the transition
-        to virtual conferences in 2021 and 2022. We also showed that the University
-        of Alabama and the University of Michigan have significantly led accepted
-        abstracts throughout the study period with University of Alabama maintaining
-        a top position following an impressive 700 percent increase in abstracts between
-        2016 and 2017. In 2023, Massachusetts General Hospital and Brigham and Women''s
-        Hospital have led absolute and percent increases in abstract submissions,
-        though this may reflect some degree of reversion following drops in abstract
-        acceptances in 2022.</p><h3 id=\"limitations-and-future-directions\">Limitations
-        and Future Directions</h3><p>This data exploration has several limitations.
-        First, our study is limited to one conference and conferences themselves are
-        only a limited component of academic productivity. However, the Academic Surgical
-        Congress is an international meeting that is well regarded, popular among
-        trainees, and has consistent multi-year data. Another limitation of our study
-        is our assumption that the first institution listed in the author block is
-        the primary institution&#x2013;a method which does not take into account multi-institutional
-        abstracts. However, we suspect this reflects the minority of the abstracts.
-        Finally, we have not fully optimized name-matching to correctly combine terms
-        like \"University of Michigan\" and \"University of Michigan Ann Arbor\".
-        However, given that most of the data currently is only for the top 20 institutions,
-        we believe the overall trends will be preserved.</p><p>In the future, we can
-        attempt to obtain more granular data on authors and institutions and optimize
-        the capture of this data for aggregated analysis. We are also researching
-        different techniques to perform string matching to fix the institution name
-        issue. We can improve the generalizability of our findings by bringing in
-        similar data from other large meetings &#x2013; such as the American College
-        of Surgeons Clinical Congress and the Society of American Gastrointestinal
-        and Endoscopic Surgeons (SAGES). We can also use the PubMed API to perform
-        similar analyses in top surgical journals such as JAMA Surgery or the Annals
-        of Surgery.</p><p>With regards to the data we have obtained, we can conduct
-        survey-based studies or focus groups with key stakeholders from institutions
-        that have demonstrated strong abstract performance during the study period
-        as well as those who have shown significant improvement. By talking to department
-        chairs, program directors, and research and education leaders we can understand
-        what steps each institution took to improve abstract acceptance (e.g. hiring
-        a new research faculty, creating a mentorship program, providing administrative
-        support for IRBs/stats etc.). Following this, we can map individual interventions
-        to improvements to understand the contribution that each can have on increased
-        academic productivity.</p><p>We have also not yet mined the abstract body
-        for themes. Using natural language processing, we can understand how themes
-        and trends of emergent research change from year to year, and even develop
-        models to predict which topics will be of interest in future works. This will
-        likely be the subject of a future data exploration.</p><p>Overall, we hope
-        to demonstrate that abstract acceptance data from a single international meeting
-        can provide interesting, meaningful data on which programs have strong research
-        infrastructure and which programs are making strides to achieve it. By studying
-        this data and improving the inputs, we can better understand whose example
-        to follow and ultimately develop a playbook that all institutions can employ
-        to maximize the academic opportunities of students and trainees.</p><h3 id=\"see-the-data\">See
-        the Data</h3><p>You can see the raw data as well as all of our code here,
-        and use this for your own studies with appropriate attribution.</p><p><a href=\"https://deepnote.com/@tejas-sathe-a73f/ASC-Data-Exploration-948ca211-bfc7-459b-9d6d-ef952a5baf32?ref=ideasurg.pub\">https://deepnote.com/@tejas-sathe-a73f/ASC-Data-Exploration-948ca211-bfc7-459b-9d6d-ef952a5baf32</a></p>","tags":["Pre-Print"],"language":"en","references":[],"blog_id":"3cxcm20","blog":{"id":"3cxcm20","title":"I.D.E.A.S.","description":"Innovation
+      string: '{"id":"153d65e1-f0e4-49a6-a969-33d2129800ba","doi":"https://doi.org/10.59350/ytvy2-59450","url":"https://www.ideasurg.pub/academic-powerhouse","title":"How
+        to Build an Academic Powerhouse: Let''s Study Who''s Doing it","summary":"Students
+        and residents aspiring for a career in academic surgery are looking for training
+        programs that will help jumpstart their careers by exposing them to mentorship
+        and opportunities to conduct research. While the gold standard of academic
+        productivity (for the time being) remains peer-reviewed publications, conference
+        posters and presentations are an important secondary metric. In addition to
+        feeding eventual papers, conference talks allow trainees to practice presentation
+        skills, build...","published_at":1685768070,"updated_at":1685768070,"indexed_at":1689006804,"authors":[{"url":null,"name":"Tejas
+        S. Sathe, MD"}],"image":null,"tags":["Pre-Print"],"language":"en","reference":[],"blog_id":"3cxcm20","blog_name":"I.D.E.A.S.","blog":{"id":"3cxcm20","title":"I.D.E.A.S.","description":"Innovation
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