commonmeta-ruby 3.3.15 → 3.3.16

data/spec/fixtures/vcr_cassettes/Commonmeta_CLI/json_feed/json_feed_by_blog.yml

@@ -23,23 +23,23 @@ http_interactions:
       Cache-Control:
       - public, max-age=0, must-revalidate
       Content-Length:
-      - '162607'
+      - '26135'
       Content-Type:
       - application/json; charset=utf-8
       Date:
-      - Thu, 15 Jun 2023 20:47:10 GMT
+      - Mon, 10 Jul 2023 20:37:16 GMT
       Etag:
-      - '"6w7me0q1i23h72"'
+      - '"a986ggx9d0k3r"'
       Server:
       - Vercel
       Strict-Transport-Security:
       - max-age=63072000
       X-Matched-Path:
-      - "/api/blogs/[slug]"
+      - "/api/blogs/[[...params]]"
       X-Vercel-Cache:
       - MISS
       X-Vercel-Id:
-      - fra1::iad1::95rf9-1686862029064-f08aa4b0d0a5
+      - fra1::iad1::b9rbm-1689021435986-bb09a174a89c
       Connection:
       - close
     body:
@@ -49,91 +49,26 @@ http_interactions:
         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?alt=rss","feed_format":"application/rss+xml","home_page_url":"https://iphylo.blogspot.com/","indexed_at":"2023-02-06","modified_at":"2023-05-31T17:26:00+00:00","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Blogger","category":"Natural
-        Sciences","backlog":true,"prefix":"10.59350","items":[{"id":"https://doi.org/10.59350/btdk4-42879","uuid":"3e1278f6-e7c0-43e1-bb54-6829e1344c0d","url":"https://iphylo.blogspot.com/2022/09/the-ideal-taxonomic-journal.html","title":"The
-        ideal taxonomic journal","summary":"This is just some random notes on an “ideal”
-        taxonomic journal, inspired in part by some recent discussions on “turbo-taxonomy”
-        (e.g., https://doi.org/10.3897/zookeys.1087.76720 and https://doi.org/10.1186/1742-9994-10-15),
-        and also examples such as the Australian Journal of Taxonomy https://doi.org/10.54102/ajt.qxi3r
-        which seems well-intentioned but limited. XML One approach is to have highly
-        structured text that embeds detailed markup, and ideally a tool that generates
-        markup in XML. This is...","date_published":"2022-09-29T14:00:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>This is just some random
-        notes on an “ideal” taxonomic journal, inspired in part by some recent discussions
-        on “turbo-taxonomy” (e.g., <a href=\"https://doi.org/10.3897/zookeys.1087.76720\">https://doi.org/10.3897/zookeys.1087.76720</a>
-        and <a href=\"https://doi.org/10.1186/1742-9994-10-15\">https://doi.org/10.1186/1742-9994-10-15</a>),
-        and also examples such as the Australian Journal of Taxonomy <a href=\"https://doi.org/10.54102/ajt.qxi3r\">https://doi.org/10.54102/ajt.qxi3r</a>
-        which seems well-intentioned but limited.</p>\n<h2 id=\"xml\">XML</h2>\n<p>One
-        approach is to have highly structured text that embeds detailed markup, and
-        ideally a tool that generates markup in XML. This is the approach taken by
-        Pensoft. There is an inevitable trade-off between the burden on authors of
-        marking up text versus making the paper machine readable. In some ways this
-        seems misplaced effort given that there is little evidence that publications
-        by themselves have much value (see <a href=\"https://iphylo.blogspot.com/2021/12/the-business-of-extracting-knowledge.html\">The
-        Business of Extracting Knowledge from Academic Publications</a>). “Value”
-        in this case means as a source of data or factual statements that we can compute
-        over. Human-readable text is not a good way to convey this sort of information.</p>\n<p>It’s
-        also interesting that many editing tools are going in the opposite direction,
-        for example there are minimalist tools using <a href=\"https://en.wikipedia.org/wiki/Markdown\">Markdown</a>
-        where the goal is to <em>get out of the author’s way</em>, rather than impose
-        a way of writing. Text is written by humans for humans, so the tools should
-        be human-friendly.</p>\n<p>The idea of publishing using XML is attractive
-        in that it gives you XML that can be archived by, say, PubMed Central, but
-        other than that the value seems limited. A cursory glance at download stats
-        for journals that provide PDF and XML downloads, such as <em>PLoS One</em>
-        and <em>ZooKeys</em>, PDF is by far the more popular format. So arguably there
-        is little value in providing XML. Those who have tried to use JATS-XML as
-        an authoring tool have not had a happy time: <a href=\"https://doi.org/10.7557/15.5517\">How
-        we tried to JATS XML</a>. However, there are various tools to help with the
-        process, such as <a href=\"https://github.com/Vitaliy-1/docxToJats\">docxToJats</a>,<br>\ntexture,
-        and <a href=\"https://github.com/elifesciences/jats-xml-to-pdf\">jats-xml-to-pdf</a>
-        if this is the route one wants to take.</p>\n<h2 id=\"automating-writing-manuscripts\">Automating
-        writing manuscripts</h2>\n<p>The dream, of course, is to have a tool where
-        you store all your taxonomic data (literature, specimens, characters, images,
-        sequences, media files, etc.) and at the click of a button generate a paper.
-        Certainly some of this can be automated, much nomenclatural and specimen information
-        could be converted to human-readable text. Ideally this computer-generated
-        text would not be edited (otherwise it could get out of sync with the underlying
-        data). The text should be <a href=\"https://en.wikipedia.org/wiki/Transclusion\">transcluded</a>.
-        As an aside, one way to do this would be to include things such as lists of
-        material examined as images rather than text while the manuscript is being
-        edited. In the same way that you (probably) wouldn’t edit a photograph within
-        your text editor, you shouldn’t be editing data. When the manuscript is published
-        the data-generated portions can then be output as text.</p>\n<p>Of course
-        all of this assumes that we have taxonomic data in a database (or some other
-        storage format, including plain text and Mark-down, e.g. <a href=\"https://iphylo.blogspot.com/2022/04/obsidian-markdown-and-taxonomic-trees.html\">Obsidian,
-        markdown, and taxonomic trees</a>) that can generate outputs in the various
-        formats that we need.</p>\n<h2 id=\"archiving-data-and-images\">Archiving
-        data and images</h2>\n<p>One of the really nice things that <a href=\"http://plazi.org\">Plazi</a>
-        do is have a pipeline that sends taxonomic descriptions and images to Zenodo,
-        and similar data to GBIF. Any taxonomic journal should be able to do this.
-        Indeed, arguably each taxonomic treatment within the paper should be linked
-        to the Zenodo DOI at the time of publication. Indeed, we could imagine ultimately
-        having treatments as transclusions within the larger manuscript. Alternatively
-        we could store the treatments as parts of the larger article (rather like
-        chapters in a book), each with a CrossRef DOI. I’m still sceptical about whether
-        these treatments are as important as we make out, see <a href=\"https://iphylo.blogspot.com/2022/09/does-anyone-cite-taxonomic-treatments.html\">Does
-        anyone cite taxonomic treatments?</a>. But having machine-readable taxonomic
-        data archived and accessible is a good thing. Uploading the same data to GBIF
-        makes much of that data immediately accessible. Now that GBIF offers <a href=\"https://www.gbif.org/composition/3kQFinjwHbCGZeLb5OhwN2/gbif-hosted-portals\">hosted
-        portals</a> there is the possibility of having custom interfaces to data from
-        a particular journal.</p>\n<h2 id=\"name-and-identifier-registration\">Name
-        and identifier registration</h2>\n<p>We would also want automatic registration
-        of new taxonomic names, for which there are pipelines (see “A common registration-to-publication
-        automated pipeline for nomenclatural acts for higher plants (International
-        Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank)”
-        <a href=\"https://doi.org/10.3897/zookeys.550.9551\">https://doi.org/10.3897/zookeys.550.9551</a>).
-        These pipelines do not seem to be documented in much detail, and the data
-        formats differ across registration agencies (e.g., IPNI and ZooBank). For
-        example, ZooBank seems to require TaxPub XML.</p>\n<p>Registration of names
-        and identifiers, especially across multiple registration agencies (ZooBank,
-        CrossRef, DataCite, etc.) requires some coordination, especially when one
-        registration agency requires identifiers from another.</p>\n<h2 id=\"summary\">Summary</h2>\n<p>If
-        data is key, then the taxonomic paper itself becomes something of a wrapper
-        around that data. It still serves the function of being human-readable, providing
-        broader context for the work, and as an archive that conforms to currently
-        accepted ways to publish taxonomic names. But in some ways it is the last
-        interesting part of the process.</p>\n<blockquote>\n<p>Written with <a href=\"https://stackedit.io/\">StackEdit</a>.</p>\n</blockquote>","tags":[],"language":"en","references":null},{"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
+        Attribution 4.0 International license</a>.","language":"en","favicon":null,"feed_url":"https://iphylo.blogspot.com/feeds/posts/default","current_feed_url":null,"feed_format":"application/atom+xml","home_page_url":"https://iphylo.blogspot.com/","indexed_at":"2023-02-06","modified_at":"2023-06-17T15:38:20+00:00","license":"https://creativecommons.org/licenses/by/4.0/legalcode","generator":"Blogger
+        7.00","category":"Natural Sciences","backlog":true,"prefix":"10.59350","expired":null,"items":[{"id":"37538c38-66e6-4ac4-ab5c-679684622ade","doi":"https://doi.org/10.59350/2b1j9-qmw12","url":"https://iphylo.blogspot.com/2022/05/round-trip-from-identifiers-to.html","title":"Round
+        trip from identifiers to citations and back again","summary":"Note to self
+        (basically rewriting last year''s Finding citations of specimens). Bibliographic
+        data supports going from identifier to citation string and back again, so
+        we can do a \"round trip.\" 1. Given a DOI we can get structured data with
+        a simple HTTP fetch, then use a tool such as citation.js to convert that data
+        into a human-readable string in a variety of formats. Identifier ⟶ Structured
+        data ⟶ Human readable string 10.7717/peerj-cs.214 HTTP with...","published_at":1653669240,"updated_at":1653669259,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["citation","GBIF","material examined","specimen
+        codes"],"language":"en","reference":[]},{"id":"545c177f-cea5-4b79-b554-3ccae9c789d7","doi":"https://doi.org/10.59350/d3dc0-7an69","url":"https://iphylo.blogspot.com/2021/10/reflections-on-macroscope-tool-for-21st.html","title":"Reflections
+        on \"The Macroscope\" - a tool for the 21st Century?","summary":"This is a
+        guest post by Tony Rees. It would be difficult to encounter a scientist, or
+        anyone interested in science, who is not familiar with the microscope, a tool
+        for making objects visible that are otherwise too small to be properly seen
+        by the unaided eye, or to reveal otherwise invisible fine detail in larger
+        objects. A select few with a particular interest in microscopy may also have
+        encountered the Wild-Leica \"Macroscope\", a specialised type of benchtop
+        microscope optimised for...","published_at":1633610280,"updated_at":1633688782,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["guest post","macroscope"],"language":"en","reference":[]},{"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
@@ -141,563 +76,24 @@ 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":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (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":null},{"id":"https://doi.org/10.59350/92rdb-5fe58","uuid":"d33d4f49-b281-4997-9eb9-dbad1e52d9bd","url":"https://iphylo.blogspot.com/2022/09/local-global-identifiers-for.html","title":"Local
-        global identifiers for decentralised wikis","summary":"I''ve been thinking
-        a bit about how one could use a Markdown wiki-like tool such as Obsidian to
-        work with taxonomic data (see earlier posts Obsidian, markdown, and taxonomic
-        trees and Personal knowledge graphs: Obsidian, Roam, Wikidata, and Xanadu).
-        One \"gotcha\" would be how to name pages. If we treat the database as entirely
-        local, then the page names don''t matter, but what if we envisage sharing
-        the database, or merging it with others (for example, if we divided a taxon
-        up into chunks, and...","date_published":"2022-09-08T16:09:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>I''ve been thinking a bit
-        about how one could use a Markdown wiki-like tool such as Obsidian to work
-        with taxonomic data (see earlier posts <a href=\"https://iphylo.blogspot.com/2022/04/obsidian-markdown-and-taxonomic-trees.html\">Obsidian,
-        markdown, and taxonomic trees</a> and <a href=\"https://iphylo.blogspot.com/2020/08/personal-knowledge-graphs-obsidian-roam.html\">Personal
-        knowledge graphs: Obsidian, Roam, Wikidata, and Xanadu</a>).</p>\n\n<p>One
-        \"gotcha\" would be how to name pages. If we treat the database as entirely
-        local, then the page names don''t matter, but what if we envisage sharing
-        the database, or merging it with others (for example, if we divided a taxon
-        up into chunks, and different people worked on those different chunks)? </p>\n\n<p>This
-        is the attraction of globally unique identifiers. You and I can independently
-        work on the same thing, such as data linked to scientific paper, safe in the
-        knowledge that if we both use the DOI for that paper we can easily combine
-        what we''ve done. But global identifiers can also be a pain, especially if
-        we need to use a service to look them up (\"is there a DOI for this paper?\",
-        \"what is the LSID for this taxonomic name?\").</p>\n\n<p>Life would be easier
-        if we could generate identifiers \"locally\", but had some assurance that
-        they would be globally unique, and that anyone else generating an identifier
-        for the same thing would arrive at the same identifier (this eliminates things
-        such as <a href=\"https://en.wikipedia.org/wiki/Universally_unique_identifier\">UUIDs</a>
-        which are intentionally designed to prvent people genrrating the same identifier).
-        One approach is \"content addressing\" (see, e.g. <a href=\"https://web.archive.org/web/20210514054054/https://bentrask.com/notes/content-addressing.html\">Principles
-        of Content Addressing</a> - dead link but in the Wayabck Machine, see also
-        <a href=\"https://github.com/btrask/stronglink\">btrask/stronglink</a>). For
-        example, we can generate a cryptographic hash of a file (such as a PDF) and
-        use that as the identifier.</p>\n\n<p>Now the problem is that we have globally
-        unique, but ugly and unfriendly identifiers (such as \"6c98136eba9084ea9a5fc0b7693fed8648014505\").
-        What we need are nice, easy to use identifiers we can use as page names. <a
-        href=\"https://species.wikimedia.org/wiki/Main_Page\">Wikispecies</a> serves
-        as a possible role model, where taxon names serve as page names, as do simplified
-        citations (e.g., authors and years). This model runs into the problem that
-        taxon names aren''t unique, nor are author + year combinations. In Wikispecies
-        this is resolved by having a centralised database where it''s first come,
-        first served. If there is a name clash you have to create a new name for your
-        page. This works, but what if you have multiple databases un by different
-        people? How do we ensure the identifiers are the same?</p>\n\n<p>Then I remembered
-        Roger Hyam''s flight of fantasy over a decade ago: <a href=\"http://www.hyam.net/blog/archives/1007\">SpeciesIndex.org
-        – an impractical, practical solution</a>. He proposed the following rules
-        to generate a unique URI for a taxonomic name:\n\n<ul>\n  <li>The URI must
-        start with \"http://speciesindex.org\" followed by one or more of the following
-        separated by slashes.</li>\n\n  <li>First word of name. Must only contain
-        letters. Must not be the same as one of the names of the nomenclatural codes
-        (icbn or iczn). Optional but highly recommended.</li> \n\n  <li>Second word
-        of name. Must only contain letters and not be a nomenclatural code name. Optional.</li>
-        \n\n  <li>Third word of name. Must only contain letters and not be a nomenclatural
-        code name. Optional.</li> \n\n  <li>Year of publication. Must be an integer
-        greater than 1650 and equal to or less than the current year. If this is an
-        ICZN name then this should be the year the species (epithet) was published
-        as is commonly cited after the name. If this is an ICBN name at species or
-        below then it is the date of the combination. Optional. Recommended for zoological
-        names if known. Not recommended for botanical names unless there is a known
-        problem with homonyms in use by non-taxonomists.</li>\n  \n<li>Nomenclatural
-        code governing the name of the taxon. Currently this must be either ''icbn''
-        or ''iczn''. This may be omitted if the code is unknown or not relevant. Other
-        codes may be added to this list.</li> \n  <li>Qualifier This must be a Version
-        4 RFC-4122 UUID. Optional. Used to generate a new independent identifier for
-        a taxon for which the conventional name is unknown or does not exist or to
-        indicate a particular taxon concept that bears the embedded name.</li>\n\n  <li>The
-        whole speciesindex.org URI string should be considered case\nsensitive. Everything
-        should be lower case apart from the first letter of words that are specified
-        as having upper case in their relevant codes e.g. names at and above the rank
-        of genus.</li>\n</ul>\n</p>\n\n<p>Roger is basically arging that while names
-        aren''t unique (i.e., we have homonyms such as <i>Abronia</i>) they are pretty
-        close to being so, and with a few tweaks we can come up with a unique representation.
-        Another way to think about this if we had a database of all taxonomics, we
-        could construct a <a href=\"https://en.wikipedia.org/wiki/Trie\">trie</a>
-        and for each name find the shortest set of name parts (genus, species, etc),
-        year, and code that gave us a unique string for that name. In many cases the
-        species name may be all we need, in other cases we may need to add year and/or
-        nomenclatural code to arrive at a unique string. \n\n</p>\n\n<p>What about
-        bibliographic references? Well many of us will have databases (e.g., Endnote,
-        Mendeley, Zotero, etc.) which generate \"cite keys\". These are typically
-        short, memorable identifiers for a reference that are unique within that database.
-        There is an interesting discussion on the <a href=\"https://discourse.jabref.org/t/universal-citekey-generator/2441/2\">JabRef
-        forum</a> regarding a \"Universal Citekey Generator\", and source code is
-        available <a href=\"https://github.com/cparnot/universal-citekey-js\">cparnot/universal-citekey-js</a>.
-        I''ve yet to explore this in detail, but it looks a promising way to generate
-        unique identifiers from basic metadata (echos of more elaborate schemes such
-        as <a href=\"https://en.wikipedia.org/wiki/Serial_Item_and_Contribution_Identifier\">SICIs</a>).
-        For example,\n\n<blockquote>Senna AR, Guedes UN, Andrade LF, Pereira-Filho
-        GH. 2021. A new species of amphipod Pariphinotus Kunkel, 1910 (Amphipoda:
-        Phliantidae) from Southwestern Atlantic. Zool Stud 60:57. doi:10.6620/ZS.2021.60-57.</blockquote>\n\nbecomes
-        \"Senna:2021ck\". So if two people have the same, core, metadata for a paper
-        they can generate the same key.</p>\n\n<p>Hence it seems with a few conventions
-        (and maybe some simple tools to support them) we could have decentralised
-        wiki-like tools that used the same identifiers for the same things, and yet
-        those identfiiers were short and human-friendly.</p>","tags":["citekey","identfiiers","markdown","obsidian","Roger
-        Hyam"],"language":"en","references":null},{"id":"https://doi.org/10.59350/j77nc-e8x98","uuid":"c6b101f4-bfbc-4d01-921d-805c43c85757","url":"https://iphylo.blogspot.com/2022/08/linking-taxonomic-names-to-literature.html","title":"Linking
-        taxonomic names to the literature","summary":"Just some thoughts as I work
-        through some datasets linking taxonomic names to the literature. In the diagram
-        above I''ve tried to capture the different situatios I encounter. Much of
-        the work I''ve done on this has focussed on case 1 in the diagram: I want
-        to link a taxonomic name to an identifier for the work in which that name
-        was published. In practise this means linking names to DOIs. This has the
-        advantage of linking to a citable indentifier, raising questions such as whether
-        citations...","date_published":"2022-08-22T17:19:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"Just some thoughts as I work
-        through some datasets linking taxonomic names to the literature.\n\n<div class=\"separator\"
-        style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5ZkbnumEWKZpf0isei_hUJucFlOOK08-SKnJknD8B4qhAX36u-vMQRnZdhRJK5rPb7HNYcnqB7qE4agbeStqyzMkWHrzUj14gPkz2ohmbOVg8P_nHo0hM94PD1wH3SPJsaLAumN8vih3ch9pjH2RaVWZBLwwhGhNu0FS1m5z6j5xt2NeZ4w/s2140/linking%20to%20names144.jpg\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" height=\"600\" data-original-height=\"2140\" data-original-width=\"1604\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5ZkbnumEWKZpf0isei_hUJucFlOOK08-SKnJknD8B4qhAX36u-vMQRnZdhRJK5rPb7HNYcnqB7qE4agbeStqyzMkWHrzUj14gPkz2ohmbOVg8P_nHo0hM94PD1wH3SPJsaLAumN8vih3ch9pjH2RaVWZBLwwhGhNu0FS1m5z6j5xt2NeZ4w/s600/linking%20to%20names144.jpg\"/></a></div>\n\n<p>In
-        the diagram above I''ve tried to capture the different situatios I encounter.
-        Much of the work I''ve done on this has focussed on case 1 in the diagram:
-        I want to link a taxonomic name to an identifier for the work in which that
-        name was published. In practise this means linking names to DOIs. This has
-        the advantage of linking to a citable indentifier, raising questions such
-        as whether citations of taxonmic papers by taxonomic databases could become
-        part of a <a href=\"https://iphylo.blogspot.com/2022/08/papers-citing-data-that-cite-papers.html\">taxonomist''s
-        Google Scholar profile</a>.</p>\n\n<p>In many taxonomic databases full work-level
-        citations are not the norm, instead taxonomists cite one or more pages within
-        a work that are relevant to a taxonomic name. These \"microcitations\" (what
-        the U.S. legal profession refer to as \"point citations\" or \"pincites\",  see
-        <a href=\"https://rasmussen.libanswers.com/faq/283203\">What are pincites,
-        pinpoints, or jump legal references?</a>) require some work to map to the
-        work itself (which is typically the thing that has a citatble identifier such
-        as a DOI).</p>\n\n<p>Microcitations (case 2 in the diagram above) can be quite
-        complex. Some might simply mention a single page, but others might list a
-        series of (not necessarily contiguous) pages, as well as figures, plates etc.
-        Converting these to citable identifiers can be tricky, especially as in most
-        cases we don''t have page-level identifiers. The Biodiversity Heritage Library
-        (BHL) does have URLs for each scanned page, and we have a standard for referring
-        to pages in a PDF (<code>page=&lt;pageNum&gt;</code>, see <a href=\"https://datatracker.ietf.org/doc/html/rfc8118\">RFC
-        8118</a>). But how do we refer to a set of pages? Do we pick the first page?
-        Do we try and represent a set of pages, and if so, how?</p>\n\n<p>Another
-        issue with page-level identifiers is that not everything on a given page may
-        be relevant to the taxonomic name. In case 2 above I''ve shaded in the parts
-        of the pages and figure that refer to the taxonomic name. An example where
-        this can be problematic is the recent test case I created for BHL where a
-        page image was included for the taxonomic name <a href=\"https://www.gbif.org/species/195763322\"><i>Aphrophora
-        impressa</i></a>. The image includes the species description and a illustration,
-        as well as text that relates to other species.</p>\n\n<div class=\"separator\"
-        style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1SAv1XiVBPHXeMLPfdsnTh4Sj4m0AQyqjXM0faXyvbNhBXFDl7SawjFIkMo3qz4RQhDEyZXkKAh5nF4gtfHbVXA6cK3NJ46CuIWECC6HmJKtTjoZ0M3QQXvLY_X-2-RecjBqEy68M0cEr0ph3l6KY51kA9BvGt9d4id314P71PBitpWMATg/s3467/https---www.biodiversitylibrary.org-pageimage-29138463.jpeg\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" height=\"400\" data-original-height=\"3467\" data-original-width=\"2106\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1SAv1XiVBPHXeMLPfdsnTh4Sj4m0AQyqjXM0faXyvbNhBXFDl7SawjFIkMo3qz4RQhDEyZXkKAh5nF4gtfHbVXA6cK3NJ46CuIWECC6HmJKtTjoZ0M3QQXvLY_X-2-RecjBqEy68M0cEr0ph3l6KY51kA9BvGt9d4id314P71PBitpWMATg/s400/https---www.biodiversitylibrary.org-pageimage-29138463.jpeg\"/></a></div>\n\n<p>Given
-        that not everything on a page need be relevant, we could extract just the
-        relevant blocks of text and illustrations (e.g., paragraphs of text, panels
-        within a figure, etc.) and treat that set of elements as the thing to cite.
-        This is, of course, what <a href=\"http://plazi.org\">Plazi</a> are doing.
-        The set of extracted blocks is glued together as a \"treatment\", assigned
-        an identifier (often a DOI), and treated as a citable unit. It would be interesting
-        to see to what extent these treatments are actually cited, for example, do
-        subsequent revisions that cite work that include treatments cite those treatments,
-        or just the work itself? Put another way, are we creating <a href=\"https://iphylo.blogspot.com/2012/09/decoding-nature-encode-ipad-app-omg-it.html\">\"threads\"</a>
-        between taxonomic revisions?</p>\n\n<p>One reason for these notes is that
-        I''m exploring uploading taxonomic name - literature links to <a href=\"https://www.checklistbank.org\">ChecklistBank</a>
-        and case 1 above is easy, as is case 3 (if we have treatment-level identifiers).
-        But case 2 is problematic because we are linking to a set of things that may
-        not have an identifier, which means a decision has to be made about which
-        page to link to, and how to refer to that page.</p>","tags":[],"language":"en","references":null},{"id":"https://doi.org/10.59350/w18j9-v7j10","uuid":"d811172e-7798-403c-a83d-3d5317a9657e","url":"https://iphylo.blogspot.com/2022/08/papers-citing-data-that-cite-papers.html","title":"Papers
-        citing data that cite papers: CrossRef, DataCite, and the Catalogue of Life","summary":"Quick
-        notes to self following on from a conversation about linking taxonomic names
-        to the literature. Is there a way to turn those links into countable citations
-        (even if just one per database) for Google Scholar?&mdash; Wayne Maddison
-        (@WayneMaddison) August 3, 2022 There are different sorts of citation:  Paper
-        cites another paper  Paper cites a dataset  Dataset cites a paper Citation
-        type (1) is largely a solved problem (although there are issues of the ownership
-        and use of this...","date_published":"2022-08-03T11:33:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"Quick notes to self following
-        on from a conversation about linking taxonomic names to the literature.\n\n<blockquote
-        class=\"twitter-tweet\"><p lang=\"en\" dir=\"ltr\">Is there a way to turn
-        those links into countable citations (even if just one per database) for Google
-        Scholar?</p>&mdash; Wayne Maddison (@WayneMaddison) <a href=\"https://twitter.com/WayneMaddison/status/1554644747406348288?ref_src=twsrc%5Etfw\">August
-        3, 2022</a></blockquote> <script async src=\"https://platform.twitter.com/widgets.js\"
-        charset=\"utf-8\"></script>\n\nThere are different sorts of citation:\n\n<ol>\n  <li>Paper
-        cites another paper</li>\n  <li>Paper cites a dataset</li>\n  <li>Dataset
-        cites a paper</li>\n</ol>\n\nCitation type (1) is largely a solved problem
-        (although there are issues of the ownership and use of this data, see e.g.
-        <a href=\"https://iphylo.blogspot.com/2020/07/zootaxa-has-no-impact-factor.html\">Zootaxa
-        has no impact factor</a>.\n\nCitation type (2) is becoming more widespread
-        (but not perfect as GBIF''s <a href=\"https://twitter.com/search?q=%23citethedoi&src=typed_query\">#citethedoi</a>
-        campaign demonstrates. But the idea is well accepted and there are guides
-        to how to do it, e.g.:\n\n<blockquote>\nCousijn, H., Kenall, A., Ganley, E.
-        et al. A data citation roadmap for scientific publishers. Sci Data 5, 180259
-        (2018). <a href=\"https://doi.org/10.1038/sdata.2018.259\">https://doi.org/10.1038/sdata.2018.259</a>\n</blockquote>\n\nHowever,
-        things do get problematic because most (but not all) DOIs for publications
-        are managed by CrossRef, which has an extensive citation database linking
-        papers to other paopers. Most datasets have DataCite DOIs, and DataCite manages
-        its own citations links, but as far as I''m aware these two systems don''t
-        really taklk to each other.\n\nCitation type (3) is the case where a database
-        is largely based on the literature, which applies to taxonomy. Taxonomic databases
-        are essentially collections of literature that have opinions on taxa, and
-        the database may simply compile those (e.g., a nomenclator), or come to some
-        view on the applicability of each name. In an ideal would, each reference
-        included in a taxonomic database would gain a citation, which would help better
-        reflect the value of that work (a long standing bone of contention for taxonomists).\n\nIt
-        would be interesting to explore these issues further. CrossRef and DataCite
-        do share <a href=\"https://www.crossref.org/services/event-data/\">Event Data</a>
-        (see also <a href=\"https://support.datacite.org/docs/eventdata-guide\">DataCite
-        Event Data</a>). Can this track citations of papers by a dataset?\n  \n  \nMy
-        take on Wayne''s question:\n\n<blockquote>\n  Is there a way to turn those
-        links into countable citations (even if just one per database) for Google
-        Scholar?\n</blockquote>\n\nis that he''s is after type 3 citations, which
-        I don''t think we have a way to handle just yet (but I''d need to look at
-        Event Data a bit more). Google Scholar is a black box, and the academic coimmunity''s
-        reliance on it for metrics is troubling. But it would be interetsing to try
-        and figure out if there is a way to get Google Scholar to index the citations
-        of taxonomic papers by databases. For instance, the <a href=\"https://www.catalogueoflife.org/\">Catalogue
-        of Life</a> has an ISSN <a href=\"https://portal.issn.org/resource/ISSN/2405-884X\">2405-884X</a>
-        so it can be treated as a publication. At the moment its web pages have lots
-        of identifiers for people managing data and their organisations (lots of <a
-        href=\"https://orcid.org\">ORCIDs</a> and <a href=\"https://ror.org\">RORs</a>,
-        and DOIs for individual datasets (e.g., <a href=\"https://www.checklistbank.org/dataset/9828/about\">checklistbank.org</a>)
-        but precious little in the way of DOIs for publications (or, indeed, ORCIDs
-        for taxonomists). What would it take for taxonomic publications in the Catalogue
-        of Life to be treated as first class citations?","tags":["Catalogue of Life","citation","CrossRef","DataCite","DOI"],"language":"en","references":null},{"id":"https://doi.org/10.59350/ws094-1w310","uuid":"6bed78ec-0029-4096-b1c3-48a55a9fdb3b","url":"https://iphylo.blogspot.com/2023/04/chatgpt-of-course.html","title":"ChatGPT,
+        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":[]},{"id":"6bed78ec-0029-4096-b1c3-48a55a9fdb3b","doi":"https://doi.org/10.59350/ws094-1w310","url":"https://iphylo.blogspot.com/2023/04/chatgpt-of-course.html","title":"ChatGPT,
         of course","summary":"I haven’t blogged for a while, work and other reasons
         have meant I’ve not had much time to think, and mostly I blog to help me think.
         ChatGPT is obviously a big thing at the moment, and once we get past the moral
         panic (“students can pass exams using AI!”) there are a lot of interesting
-        possibilities to explore. Inspired by essays such as How Q&amp;A systems based
+        possibilities to explore. Inspired by essays such as How Q&A systems based
         on large language models (eg GPT4) will change things if they become the dominant
-        search paradigm — 9 implications for libraries...","date_published":"2023-04-03T12:52:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>I haven’t blogged for a
-        while, work and <a href=\"https://iphylo.blogspot.com/2023/03/dugald-stuart-page-1936-2022.html\">other
-        reasons</a> have meant I’ve not had much time to think, and mostly I blog
-        to help me think.</p>\n<p>ChatGPT is obviously a big thing at the moment,
-        and once we get past the moral panic (“students can pass exams using AI!”)
-        there are a lot of interesting possibilities to explore. Inspired by essays
-        such as <a href=\"https://medium.com/@aarontay/how-q-a-systems-based-on-large-language-models-eg-gpt4-will-change-things-if-they-become-the-norm-c7cf62736ba\">How
-        Q&amp;A systems based on large language models (eg GPT4) will change things
-        if they become the dominant search paradigm — 9 implications for libraries</a>
-        and <a href=\"https://about.sourcegraph.com/blog/cheating-is-all-you-need\">Cheating
-        is All You Need</a>, as well as [<a href=\"https://paul-graham-gpt.vercel.app/\">Paul
-        Graham GPT</a>](<a href=\"https://paul-graham-gpt.vercel.app\">https://paul-graham-gpt.vercel.app</a>)
-        I thought I’d try a few things and see where this goes.</p>\n<p>ChatGPT can
-        do some surprising things.</p>\n<h4 id=\"parse-bibliographic-data\">Parse
-        bibliographic data</h4>\n<p>I spend a LOT of time working with bibliographic
-        data, trying to parse it into structured data. ChatGPT can do this:</p>\n\n<div
-        class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2bA-Xk6D2wfexP0cs-U3AQa534hNW7J06I0avM82WD3dZSiRvXyHFScv3Hb8QfKKp1fk4GU4olhv1BOq8Pqu4IJgptlBap3xcLI1bFJwB3EOmHKxqf4iy2exJy4vwZ2n4I0U0JVui4Xmhvdy3mTbMSXCRbmCglNFULi5oQEhtPVG4gLJjdw/s924/Screenshot%202023-04-03%20at%2012.59.30.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" height=\"400\" data-original-height=\"924\" data-original-width=\"738\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2bA-Xk6D2wfexP0cs-U3AQa534hNW7J06I0avM82WD3dZSiRvXyHFScv3Hb8QfKKp1fk4GU4olhv1BOq8Pqu4IJgptlBap3xcLI1bFJwB3EOmHKxqf4iy2exJy4vwZ2n4I0U0JVui4Xmhvdy3mTbMSXCRbmCglNFULi5oQEhtPVG4gLJjdw/s400/Screenshot%202023-04-03%20at%2012.59.30.png\"/></a></div>\n\n<p>Note
-        that it does more than simply parse the strings, it expands journal abbreviations
-        such as “J. Malay Brch. R. Asiat. Soc.” to the full name “Journal of the Malayan
-        Branch of the Royal Asiatic Society”.  So we can get clean, parsed data in
-        a range of formats.</p>\n<h4 id=\"parse-specimens\">Parse specimens</h4>\n<p>Based
-        on the success with parsing bibliographic strings I wondered how well it could
-        handle citation software specimens (“material examined”). Elsewhere I’ve been
-        critical of Plazi’s ability to do this, see <a href=\"https://iphylo.blogspot.com/2021/10/problems-with-plazi-parsing-how.html\">Problems
-        with Plazi parsing: how reliable are automated methods for extracting specimens
-        from the literature?</a>.</p>\n<p>For example, given this specimen record
-        on p. 130 of <a href=\"https://doi.org/10.5852/ejt.2021.775.1553\">doi:10.5852/ejt.2021.775.1553</a></p>\n<blockquote>\n<p>LAOS
-        • Kammoune Province, Bunghona Market, 7 km Nof Xe Bangfai River;<br>\n17.13674°
-        N, 104.98591° E; E. Jeratthitikul, K. Wisittikoson, A. Fanka, N. Wutthituntisil
-        and P. Prasankok leg.; sold by local people;<br>\nMUMNH-UNI2831.</p>\n</blockquote>\n<p>ChatGPT
-        extracted a plausible Darwin Core record:</p>\n\n<div class=\"separator\"
-        style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIwVYuPXl47t1uSpJ3xpbsIT60UUWeKTKSBpIQgD8L2gkj_fuNf4sZKR76JgsfVYYHPs9G9VoM-caUhG1P3irMyB6erSYwYI5LDlLkxdrAFWdbY3ExDs34nMVOF0tq-NBtsDKMZsSJWjhJaGt9v3dtAqWvRyVMNZ46eG2sRhJTICTkFghKtw/s901/Screenshot%202023-04-03%20at%2013.30.54.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" height=\"400\" data-original-height=\"901\" data-original-width=\"764\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgIwVYuPXl47t1uSpJ3xpbsIT60UUWeKTKSBpIQgD8L2gkj_fuNf4sZKR76JgsfVYYHPs9G9VoM-caUhG1P3irMyB6erSYwYI5LDlLkxdrAFWdbY3ExDs34nMVOF0tq-NBtsDKMZsSJWjhJaGt9v3dtAqWvRyVMNZ46eG2sRhJTICTkFghKtw/s400/Screenshot%202023-04-03%20at%2013.30.54.png\"/></a></div>\n\n<p>I’ve
-        been experimenting with parsing specimen records using the same machine learning
-        approach for bibliographic data (e.g., <a href=\"https://iphylo.blogspot.com/2021/07/citation-parsing-released.html\">Citation
-        parsing tool released</a>), perhaps it’s time to rethink that idea.</p>\n<h4
-        id=\"correct-ocr-errors\">Correct OCR errors</h4>\n<p>OCR errors are a well
-        known limitation of the Biodiversity Heritage Library (BHL), see for example
-        <a href=\"https://blog.biodiversitylibrary.org/2022/07/ocr-improvements-early-analysis.html\">OCR
-        Improvements: An Early Analysis</a>. Given that ChatGPT is built on top of
-        a large language model it seems obvious to see how it handles OCR errors.
-        I tried the following snippet of text from <a href=\"https://www.biodiversitylibrary.org/page/4312227\">BHL
-        page 4312227</a>:</p>\n<blockquote>\n<p>i BREVIORA No. 185</p>\n<p>Jiiaii
-        Jr., 16, who always join him and Hedriek in th(&gt; search  for<br>\nfrogs.
-        Iloraeio Mayorga, research assistant to tlie author,  has also<br>\nbeen (wtreniely
-        useful, not only in field work, but also  in the<br>\ntedious curatorial and
-        laboratory work that usually fol-  lows. Dr.<br>\nJohn Randall kindly took
-        tlie photouraplis of E.  hedricki, and the<br>\nGaliiiaues family of San Juan
-        made their El  Verde house available as<br>\na (MMiter of activities for the
-        colleetiuff  party. To all these<br>\njx’opic, the autlioi- feels (iee])ly
-        indebted.</p>\n<p>Elet’tiierodactylus iiKnRrcKi s]). n.</p>\n<p>Type. Museum
-        of Coniparative Zoology Xo. ;}()!)()8, c^ from  El Verde,<br>\nwest flank
-        of El Yuiuinc Puerto Hico. I.IOO ft.  Coll. J. A. Kivero,<br>\n11 Aug-. I!)(i2.</p>\n</blockquote>\n<p>ChatGPT
-        returns this:</p>\n<blockquote>\n<p>i BREVIORA No. 185</p>\n<p>Juan Jr., 16,
-        who always joins him and Hedrick in the search for<br>\nfrogs. Horacio Mayorga,
-        research assistant to the author, has also<br>\nbeen extremely useful, not
-        only in field work, but also in the tedious<br>\ncuratorial and laboratory
-        work that usually follows. Dr. John Randall<br>\nkindly took the photographs
-        of E. hedricki, and the Galinanes family<br>\nof San Juan made their El Verde
-        house available as a center of<br>\nactivities for the collecting party. To
-        all these people, the author<br>\nfeels deeply indebted.</p>\n<p>Eleutherodactylus
-        hedricki sp. n.</p>\n<p>Type. Museum of Comparative Zoology No. 30908, c?
-        from El Verde, west<br>\nflank of El Yunque, Puerto Rico. 1100 ft. Coll. J.
-        A. Rivero, 11 Aug.<br>\n1962.</p>\n</blockquote>\n\n<div class=\"separator\"
-        style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibZLxXSTdt64SMhfqS8NCcLOxbVaFmkhMQx0yEUWcm696EL6k2_VgxZFEDT-SEqOChmwDggoQLkuU6DpcOF_d-nkQRKzQLt65WKfkFlIzDRV9LVrDqmu-D0OZl1p5Vva4QUdvDb3JpeKPPDXZ-BcZqq8V4PyGepxlnwtt7-q4Sg6_aHD58gw/s859/Screenshot%202023-04-03%20at%2013.07.53.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"510\" data-original-width=\"859\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibZLxXSTdt64SMhfqS8NCcLOxbVaFmkhMQx0yEUWcm696EL6k2_VgxZFEDT-SEqOChmwDggoQLkuU6DpcOF_d-nkQRKzQLt65WKfkFlIzDRV9LVrDqmu-D0OZl1p5Vva4QUdvDb3JpeKPPDXZ-BcZqq8V4PyGepxlnwtt7-q4Sg6_aHD58gw/s400/Screenshot%202023-04-03%20at%2013.07.53.png\"/></a></div>\n\n<p>Comparing
-        this to the scanned image ChatGPT it does pretty well, for example the gobbledegook
-        “Elet’tiierodactylus iiKnRrcKi” is correctly translated as “Eleutherodactylus
-        hedricki”.  Running all of BHL through ChatGPT probably isn’t feasible, but
-        one could imagine targeted cleaning of key papers.</p>\n<h4 id=\"summary\">Summary</h4>\n<p>These
-        small experiments are fairly trivial, but they are the sort of tedious tasks
-        that would otherwise require significant programming (or other resources)
-        to solve. But ChatGPT can do rather more, as I hope to discuss in the next
-        post.</p>\n<blockquote>\n<p>Written with <a href=\"https://stackedit.io/\">StackEdit</a>.</p>\n</blockquote>","tags":[],"language":"en","references":null},{"id":"https://doi.org/10.59350/7esgr-61v1","uuid":"96fa91d5-459c-482f-aa38-dda6e0a30e20","url":"https://iphylo.blogspot.com/2022/01/large-graph-viewer-experiments.html","title":"Large
-        graph viewer experiments","summary":"I keep returning to the problem of viewing
-        large graphs and trees, which means my hard drive has accumulated lots of
-        failed prototypes. Inspired by some recent discussions on comparing taxonomic
-        classifications I decided to package one of these (wildly incomplete) prototypes
-        up so that I can document the idea and put the code somewhere safe. Very cool,
-        thanks for sharing this-- the tree diff is similar to what J Rees has been
-        cooking up lately with his &#39;cl diff&#39; tool. I&#39;ll tag...","date_published":"2022-01-02T11:25:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>I keep returning to the
-        problem of viewing large graphs and trees, which means my hard drive has accumulated
-        lots of failed prototypes. Inspired by some recent discussions on comparing
-        taxonomic classifications I decided to package one of these (wildly incomplete)
-        prototypes up so that I can document the idea and put the code somewhere safe.</p>\n\n<blockquote
-        class=\"twitter-tweet\"><p lang=\"en\" dir=\"ltr\">Very cool, thanks for sharing
-        this-- the tree diff is similar to what J Rees has been cooking up lately
-        with his &#39;cl diff&#39; tool. I&#39;ll tag <a href=\"https://twitter.com/beckettws?ref_src=twsrc%5Etfw\">@beckettws</a>
-        in here too so he can see potential crossover. The goal is autogenerate diffs
-        like this as 1st step to mapping taxo name-to concept</p>&mdash; Nate Upham
-        (@n8_upham) <a href=\"https://twitter.com/n8_upham/status/1475834371131289608?ref_src=twsrc%5Etfw\">December
-        28, 2021</a></blockquote> <script async src=\"https://platform.twitter.com/widgets.js\"
-        charset=\"utf-8\"></script>\n\n<h2>Google Maps-like viewer</h2>\n\n<div class=\"separator\"
-        style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/a/AVvXsEiGDVVKGmwRi0gn-kEtpxBCUEdK-WCLBSpmkALAUDHGeTPkTSICSYVgnsj5N7zUeUfQALfFFHJJCsfeFvRULKbmqxLz51rW5hp_11dVXh-FHrnlRA7RJTA7I82l7sERF5jAjlah0LyEheVayO9nAfHTGZDuw5rnCe9iEO3dHQmA8_5AFIlJJg=s500\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"448\" data-original-width=\"500\"
-        src=\"https://blogger.googleusercontent.com/img/a/AVvXsEiGDVVKGmwRi0gn-kEtpxBCUEdK-WCLBSpmkALAUDHGeTPkTSICSYVgnsj5N7zUeUfQALfFFHJJCsfeFvRULKbmqxLz51rW5hp_11dVXh-FHrnlRA7RJTA7I82l7sERF5jAjlah0LyEheVayO9nAfHTGZDuw5rnCe9iEO3dHQmA8_5AFIlJJg=s400\"/></a></div>\n\n<p>I''ve
-        created a simple viewer that uses a tiled map viewer (like Google Maps) to
-        display a large graph. The idea is to draw the entire graph scaled to a 256
-        x 256 pixel tile. The graph is stored in a database that supports geospatial
-        queries, which means the queries to retrieve the individual tiles need to
-        display the graph at different levels of resolution are simply bounding box
-        queries to a database. I realise that this description is cryptic at best.
-        The GitHub repository <a href=\"https://github.com/rdmpage/gml-viewer\">https://github.com/rdmpage/gml-viewer</a>
-        has more details and the code itself. There''s a lot to do, especially adding
-        support for labels(!) which presents some interesting challenges (<a href=\"https://en.wikipedia.org/wiki/Level_of_detail_(computer_graphics)\">levels
-        of detail</a> and <a href=\"https://en.wikipedia.org/wiki/Cartographic_generalization\">generalization</a>).
-        The code doesn''t do any layout of the graph itself, instead I''ve used the
-        <a href=\"https://www.yworks.com/products/yed\">yEd</a> tool to compute the
-        x,y coordinates of the graph.</p>\n\n<p>Since this exercise was inspired by
-        a discussion of the <a href=\"https://www.mammaldiversity.org\">ASM Mammal
-        Diversity Database</a>, the graph I''ve used for the demonstration above is
-        the ASM classification of extant mammals. I guess I need to solve the labelling
-        issue fairly quickly!</p>","tags":["Google Maps","graph","Mammal Species of
-        the World","mammals","taxonomy"],"language":"en","references":null},{"id":"https://doi.org/10.59350/m48f7-c2128","uuid":"8aea47e4-f227-45f4-b37b-0454a8a7a3ff","url":"https://iphylo.blogspot.com/2023/04/chatgpt-semantic-search-and-knowledge.html","title":"ChatGPT,
-        semantic search, and knowledge graphs","summary":"One thing about ChatGPT
-        is it has opened my eyes to some concepts I was dimly aware of but am only
-        now beginning to fully appreciate. ChatGPT enables you ask it questions, but
-        the answers depend on what ChatGPT “knows”. As several people have noted,
-        what would be even better is to be able to run ChatGPT on your own content.
-        Indeed,  ChatGPT itself now supports this using plugins. Paul Graham GPT However,
-        it’s still useful to see how to add ChatGPT functionality to your own content
-        from...","date_published":"2023-04-03T15:30:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>One thing about ChatGPT
-        is it has opened my eyes to some concepts I was dimly aware of but am only
-        now beginning to fully appreciate. ChatGPT enables you ask it questions, but
-        the answers depend on what ChatGPT “knows”. As several people have noted,
-        what would be even better is to be able to run ChatGPT on your own content.
-        Indeed,  ChatGPT itself now supports this using <a href=\"https://openai.com/blog/chatgpt-plugins\">plugins</a>.</p>\n<h4
-        id=\"paul-graham-gpt\">Paul Graham GPT</h4>\n<p>However, it’s still useful
-        to see how to add ChatGPT functionality to your own content from scratch.
-        A nice example of this is <a href=\"https://paul-graham-gpt.vercel.app/\">Paul
-        Graham GPT</a> by <a href=\"https://twitter.com/mckaywrigley\">Mckay Wrigley</a>.
-        Mckay Wrigley took essays by Paul Graham (a well known venture capitalist)
-        and built a question and answer tool very like ChatGPT.</p>\n<iframe width=\"560\"
-        height=\"315\" src=\"https://www.youtube.com/embed/ii1jcLg-eIQ\" title=\"YouTube
-        video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write;
-        encrypted-media; gyroscope; picture-in-picture; web-share\" allowfullscreen></iframe>\n<p>Because
-        you can send a block of text to ChatGPT (as part of the prompt) you can get
-        ChatGPT to summarise or transform that information, or answer questions based
-        on that information. But there is a limit to how much information you can
-        pack into a prompt. You can’t put all of Paul Graham’s essays into a prompt
-        for example. So a solution is to do some preprocessing. For example, given
-        a question such as “How do I start a startup?” we could first find the essays
-        that are most relevant to this question, then use them to create a prompt
-        for ChatGPT. A quick and dirty way to do this is simply do a text search over
-        the essays and take the top hits. But we aren’t searching for words, we are
-        searching for answers to a question. The essay with the best answer might
-        not include the phrase “How do I start a startup?”.</p>\n<h4 id=\"semantic-search\">Semantic
-        search</h4>\n<p>Enter <a href=\"https://en.wikipedia.org/wiki/Semantic_search\">Semantic
-        search</a>. The key concept behind semantic search is that we are looking
-        for documents with similar meaning, not just similarity of text. One approach
-        to this is to represent documents by “embeddings”, that is, a vector of numbers
-        that encapsulate features of the document. Documents with similar vectors
-        are potentially related. In semantic search we take the query (e.g., “How
-        do I start a startup?”), compute its embedding, then search among the documents
-        for those with similar embeddings.</p>\n<p>To create Paul Graham GPT Mckay
-        Wrigley did the following. First he sent each essay to the OpenAI API underlying
-        ChatGPT, and in return he got the embedding for that essay (a vector of 1536
-        numbers). Each embedding was stored in a database (Mckay uses Postgres with
-        <a href=\"https://github.com/pgvector/pgvector\">pgvector</a>). When a user
-        enters a query such as “How do I start a startup?” that query is also sent
-        to the OpenAI API to retrieve its embedding vector. Then we query the database
-        of embeddings for Paul Graham’s essays and take the top five hits. These hits
-        are, one hopes, the most likely to contain relevant answers. The original
-        question and the most similar essays are then bundled up and sent to ChatGPT
-        which then synthesises an answer. See his <a href=\"https://github.com/mckaywrigley/paul-graham-gpt\">GitHub
-        repo</a> for more details. Note that we are still using ChatGPT, but on a
-        set of documents it doesn’t already have.</p>\n<h4 id=\"knowledge-graphs\">Knowledge
-        graphs</h4>\n<p>I’m a fan of knowledge graphs, but they are not terribly easy
-        to use. For example, I built a knowledge graph of Australian animals <a href=\"https://ozymandias-demo.herokuapp.com\">Ozymandias</a>
-        that contains a wealth of information on taxa, publications, and people, wrapped
-        up in a web site. If you want to learn more you need to figure out how to
-        write queries in SPARQL, which is not fun. Maybe we could use ChatGPT to write
-        the SPARQL queries for us, but it would be much more fun to be simply ask
-        natural language queries (e.g., “who are the experts on Australian ants?”).
-        I made some naïve notes on these ideas <a href=\"https://iphylo.blogspot.com/2015/09/possible-project-natural-language.html\">Possible
-        project: natural language queries, or answering “how many species are there?”</a>
-        and <a href=\"https://iphylo.blogspot.com/2019/05/ozymandias-meets-wikipedia-with-notes.html\">Ozymandias
-        meets Wikipedia, with notes on natural language generation</a>.</p>\n<p>Of
-        course, this is a well known problem. Tools such as <a href=\"http://rdf2vec.org\">RDF2vec</a>
-        can take RDF from a knowledge graph and create embeddings which could in tern
-        be used to support semantic search. But it seems to me that we could simply
-        this process a bit by making use of ChatGPT.</p>\n<p>Firstly we would generate
-        natural language statements from the knowledge graph (e.g., “species x belongs
-        to genus y and was described in z”, “this paper on ants was authored by x”,
-        etc.) that cover the basic questions we expect people to ask. We then get
-        embeddings for these (e.g., using OpenAI). We then have an interface where
-        people can ask a question (“is species x a valid species?”, “who has published
-        on ants”, etc.), we get the embedding for that question, retrieve natural
-        language statements that the closest in embedding “space”, package everything
-        up and ask ChatGPT to summarise the answer.</p>\n<p>The trick, of course,
-        is to figure out how t generate natural language statements from the knowledge
-        graph (which amounts to deciding what paths to traverse in the knowledge graph,
-        and how to write those paths is something approximating English). We also
-        want to know something about the sorts of questions people are likely to ask
-        so that we have a reasonable chance of having the answers (for example, are
-        people going to ask about individual species, or questions about summary statistics
-        such as numbers of species in  a genus, etc.).</p>\n<p>What makes this attractive
-        is that it seems a straightforward way to go from a largely academic exercise
-        (build a knowledge graph) to something potentially useful (a question and
-        answer machine). Imagine if something like the defunct BBC wildlife site (see
-        <a href=\"https://iphylo.blogspot.com/2017/12/blue-planet-ii-bbc-and-semantic-web.html\">Blue
-        Planet II, the BBC, and the Semantic Web: a tale of lessons forgotten and
-        opportunities lost</a>) revived <a href=\"https://aspiring-look.glitch.me\">here</a>
-        had a question and answer interface where we could ask questions rather than
-        passively browse.</p>\n<h4 id=\"summary\">Summary</h4>\n<p>I have so much
-        more to learn, and need to think about ways to incorporate semantic search
-        and ChatGPT-like tools into knowledge graphs.</p>\n<blockquote>\n<p>Written
-        with <a href=\"https://stackedit.io/\">StackEdit</a>.</p>\n</blockquote>","tags":[],"language":"en","references":null},{"id":"https://doi.org/10.59350/rfxj3-x6739","uuid":"6a4d5c44-f4a9-4d40-a32c-a4d5e512c55a","url":"https://iphylo.blogspot.com/2022/05/thoughts-on-treebase-dying.html","title":"Thoughts
-        on TreeBASE dying(?)","summary":"@rvosa is Naturalis no longer hosting Treebase?
-        https://t.co/MBRgcxaBmR&mdash; Hilmar Lapp (@hlapp) May 10, 2022 So it looks
-        like TreeBASE is in trouble, it''s legacy Java code a victim of security issues.
-        Perhaps this is a chance to rethink TreeBASE, assuming that a repository of
-        published phylogenies is still considered a worthwhile thing to have (and
-        I think that question is open). Here''s what I think could be done. The data
-        (individual studies with trees and data) are packaged into...","date_published":"2022-05-11T16:53:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<blockquote class=\"twitter-tweet\"><p
-        lang=\"en\" dir=\"ltr\"><a href=\"https://twitter.com/rvosa?ref_src=twsrc%5Etfw\">@rvosa</a>
-        is Naturalis no longer hosting Treebase? <a href=\"https://t.co/MBRgcxaBmR\">https://t.co/MBRgcxaBmR</a></p>&mdash;
-        Hilmar Lapp (@hlapp) <a href=\"https://twitter.com/hlapp/status/1524166490798309381?ref_src=twsrc%5Etfw\">May
-        10, 2022</a></blockquote> <script async src=\"https://platform.twitter.com/widgets.js\"
-        charset=\"utf-8\"></script>\n\n<p>So it looks like <a href=\"http://treebase.org\">TreeBASE</a>
-        is in trouble, it''s legacy Java code a victim of security issues. Perhaps
-        this is a chance to rethink TreeBASE, assuming that a repository of published
-        phylogenies is still considered a worthwhile thing to have (and I think that
-        question is open).</p>\n\n<p>Here''s what I think could be done.</p>\n\n<ol>\n<li>\nThe
-        data (individual studies with trees and data) are packaged into whatever format
-        is easiest (NEXUS, XML, JSON) and uploaded to a repository such as <a href=\"https://zenodo.org\">Zenodo</a>
-        for long term storage. They get DOIs for citability. This becomes the default
-        storage for TreeBASE.\n</li>\n<li>\nThe data is transformed into JSON and
-        indexed using Elasticsearch. A simple web interface is placed on top so that
-        people can easily find trees (never a strong point of the original TreeBASE).
-        Trees are displayed natively on the web using SVG. The number one goal is
-        for people to be able to find trees, view them, and download them.\n</li>\n<li>\nTo
-        add data to TreeBASE the easiest way would be for people to upload them direct
-        to Zenodo and tag them \"treebase\". A bot then grabs a feed of these datasets
-        and adds them to the search engine in (1) above. As time allows, add an interface
-        where people upload data directly, it gets curated, then deposited in Zenodo.
-        This presupposes that there are people available to do curation. Maybe have
-        \"stars\" for the level of curation so that users know whether anyone has
-        checked the data.\n</li>\n</ol>\n\n<p>There''s lots of details to tweak, for
-        example how many of the existing URLs for studies are preserved (some URL
-        mapping), and what about the API? And I''m unclear about the relationship
-        with <a href=\"https://datadryad.org\">Dryad</a>.</p>\n\n<p>My sense is that
-        the TreeBASE code is very much of its time (10-15 years ago), a monolithic
-        block of code with SQL, Java, etc. If one was starting from scratch today
-        I don''t think this would be the obvious solution. Things have trended towards
-        being simpler, with lots of building blocks now available in the cloud. Need
-        a search engine? Just spin up a container in the cloud and you have one. More
-        and more functionality can be devolved elsewhere.</p>\n\n<p>Another other
-        issue is how to support TreeBASE. It has essentially been a volunteer effort
-        to date, with little or no funding. One reason I think having Zenodo as a
-        storage engine is that it takes care of long term sustainability of the data.</p>\n\n<p>I
-        realise that this is all wild arm waving, but maybe now is the time to reinvent
-        TreeBASE?</p>\n\n<h2>Updates</h2>\n\n<p>It''s been a while since I''ve paid
-        a lot of attention to phylogenetic databases, and it shows. There is a file-based
-        storage system for phylogenies <a href=\"https://github.com/OpenTreeOfLife/phylesystem-1\">phylesystem</a>
-        (see \"Phylesystem: a git-based data store for community-curated phylogenetic
-        estimates\" <a href=\"https://doi.org/10.1093/bioinformatics/btv276\">https://doi.org/10.1093/bioinformatics/btv276</a>)
-        that is sort of what I had in mind, although long term persistence is based
-        on GitHub rather than a repository such as Zenodo. Phylesystem uses a truly
-        horrible-looking JSON transformation of <a href=\"http://nexml.github.io\">NeXML</a>
-        (NeXML itself is ugly), and TreeBASE also supports NeXML, so some form of
-        NeXML or a JSON transformation seems the obvious storage format. It will probably
-        need some cleaning and simplification if it is to be indexed easily. Looking
-        back over the long history of TreeBASE and phylogenetic databases I''m struck
-        by how much complexity has been introduced over time. I think the tech has
-        gotten in the way sometimes (which might just be another way of saying that
-        I''m not smart enough to make sense of it all.</p>\n\n<p>So we could imagine
-        a search engine that covers both TreeBASE and <a href=\"https://tree.opentreeoflife.org/curator\">Open
-        Tree of Life studies</a>.</p>\n\n<p>Basic metadata-based searches would be
-        straightforward, and we could have a user interface that highlights the trees
-        (I think TreeBASE''s biggest search rival is a Google image search). The harder
-        problem is searching by tree structure, for which there is an interesting
-        literature without any decent implementations that I''m aware of (as I said,
-        I''ve been out of this field a while).</p>\n\n<p>So my instinct is we could
-        go a long way with simply indexing JSON (CouchDB or Elasticsearch), then need
-        to think a bit more cleverly about higher taxon and tree based searching.
-        I''ve always thought that one killer query would be not so much \"show me
-        all the trees for my taxon\" but \"show me a synthesis of the trees for my
-        taxon\". Imagine a supertree of recent studies that we could use as a summary
-        of our current knowledge, or a visualisation that summarises where there are
-        conflicts among the trees.</p>\n\n<h3>Relevant code and sites</h3>\n\n<ul>\n<li><a
-        href=\"https://github.com/rdmpage/cdaotools\">CDAO Tools</a>, see \"CDAO-Store:
-        Ontology-driven Data Integration for Phylogenetic Analysis\" <a href=\"https://doi.org/10.1186/1471-2105-12-98\">https://doi.org/10.1186/1471-2105-12-98</a></li>\n<li><a
-        href=\"https://github.com/NESCent/phylocommons\">PhyloCommons</a></li>\n</ul>","tags":["phylogeny","TreeBASE"],"language":"en","references":null},{"id":"https://doi.org/10.59350/jzvs4-r9559","uuid":"23fa1dd8-5c6b-4aa9-9cad-c6f6b14ae9e0","url":"https://iphylo.blogspot.com/2021/08/json-ld-in-wild-examples-of-how.html","title":"JSON-LD
+        search paradigm — 9 implications for libraries...","published_at":1680526320,"updated_at":1680526621,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":[],"language":"en","reference":[]},{"id":"7d814863-43b5-4faf-a475-da8de5efd3ef","doi":"https://doi.org/10.59350/m7gb7-d7c49","url":"https://iphylo.blogspot.com/2022/02/duplicate-dois-again.html","title":"Duplicate
+        DOIs (again)","summary":"This blog post provides some background to a recent
+        tweet where I expressed my frustration about the duplication of DOIs for the
+        same article. I''m going to document the details here. The DOI that alerted
+        me to this problem is https://doi.org/10.2307/2436688 which is for the article
+        Snyder, W. C., & Hansen, H. N. (1940). THE SPECIES CONCEPT IN FUSARIUM. American
+        Journal of Botany, 27(2), 64–67. This article is hosted by JSTOR at https://www.jstor.org/stable/2436688
+        which displays the DOI...","published_at":1644332760,"updated_at":1644332778,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["CrossRef","DOI","duplicates"],"language":"en","reference":[]},{"id":"23fa1dd8-5c6b-4aa9-9cad-c6f6b14ae9e0","doi":"https://doi.org/10.59350/jzvs4-r9559","url":"https://iphylo.blogspot.com/2021/08/json-ld-in-wild-examples-of-how.html","title":"JSON-LD
         in the wild: examples of how structured data is represented on the web","summary":"I''ve
         created a GitHub repository so that I can keep track of the examples of JSON-LD
         that I''ve seen being actively used, for example embedded in web sites, or
@@ -705,504 +101,95 @@ http_interactions:
         The list is by no means exhaustive, I hope to add more examples as I come
         across them. One reason for doing this is to learn what others are doing.
         For example, after looking at SciGraph''s JSON-LD I now see how an ordered
-        list can be modelled in RDF in...","date_published":"2021-08-27T13:20:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>I''ve created a GitHub repository
-        so that I can keep track of the examples of JSON-LD that I''ve seen being
-        actively used, for example embedded in web sites, or accessed using an API.
-        The repository is <a href=\"https://github.com/rdmpage/wild-json-ld\">https://github.com/rdmpage/wild-json-ld</a>.
-        The list is by no means exhaustive, I hope to add more examples as I come
-        across them.</p>\n\n<p>One reason for doing this is to learn what others are
-        doing. For example, after looking at SciGraph''s JSON-LD I now see how an
-        ordered list can be modelled in RDF in such a way that the list of authors
-        in a JSON-LD document for, say a scientific paper, is correct. By default
-        RDF has no notion of ordered lists, so if you do a SPARQL query to get the
-        authors of a paper, the order of the authors returned in the query will be
-        arbitrary. There are various ways to try and tackle this. In my Ozymandias
-        knowledge graph I used \"roles\" to represent order (see <a href=\"https://doi.org/10.7717/peerj.6739/fig-2\">Figure
-        2</a> in the Ozymandias paper). I then used properties of the role to order
-        the list of authors.</p>\n\n<p>Another approach is to use rdf:lists (see <a
-        href=\"http://www.snee.com/bobdc.blog/2014/04/rdf-lists-and-sparql.html\">RDF
-        lists and SPARQL</a> and <a href=\"https://stackoverflow.com/questions/17523804/is-it-possible-to-get-the-position-of-an-element-in-an-rdf-collection-in-sparql/17530689#17530689\">Is
-        it possible to get the position of an element in an RDF Collection in SPARQL?</a>
-        for an introduction to lists). SciGraph uses this approach. The value for
-        schema:author is not an author, but a blank node (bnode), and this bnode has
-        two predicates, rdf:first and rdf:rest. One points to an author, the other
-        points to another bnode. This pattern repeats until we encounter a value of
-        rdf:nil for rdf:rest.</p>\n\n<div class=\"separator\" style=\"clear: both;\"><a
-        href=\"https://1.bp.blogspot.com/-AESgWub1ZLQ/YSjoeo6O41I/AAAAAAAAgwg/5Edm7ZmuwL8NwxCcBvTqbI7js5nYmgggwCLcBGAsYHQ/s629/list.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" height=\"320\" data-original-height=\"629\" data-original-width=\"401\"
-        src=\"https://1.bp.blogspot.com/-AESgWub1ZLQ/YSjoeo6O41I/AAAAAAAAgwg/5Edm7ZmuwL8NwxCcBvTqbI7js5nYmgggwCLcBGAsYHQ/s320/list.png\"/></a></div>\n\n<p>This
-        introduces some complexity, but the benefit is that the JSON-LD version of
-        the RDF will have the authors in the correct order, and hence any client that
-        is using JSON will be able to treat the array of authors as ordered. Without
-        some means of ordering the client could not make this assumption, hence the
-        first author in the list might not actually be the first author of the paper.</p>","tags":["JSON-LD","RDF"],"language":"en","references":null},{"id":"https://doi.org/10.59350/zc4qc-77616","uuid":"30c78d9d-2e50-49db-9f4f-b3baa060387b","url":"https://iphylo.blogspot.com/2022/09/does-anyone-cite-taxonomic-treatments.html","title":"Does
-        anyone cite taxonomic treatments?","summary":"Taxonomic treatments have come
-        up in various discussions I''m involved in, and I''m curious as to whether
-        they are actually being used, in particular, whether they are actually being
-        cited. Consider the following quote: The taxa are described in taxonomic treatments,
-        well defined sections of scientific publications (Catapano 2019). They include
-        a nomenclatural section and one or more sections including descriptions, material
-        citations referring to studied specimens, or notes ecology and...","date_published":"2022-09-01T16:49:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<div class=\"separator\" style=\"clear:
-        both;\"><a href=\"https://zenodo.org/record/5731100/thumb100\" style=\"display:
-        block; padding: 1em 0; text-align: center; clear: right; float: right;\"><img
-        alt=\"\" border=\"0\" height=\"128\" data-original-height=\"106\" data-original-width=\"100\"
-        src=\"https://zenodo.org/record/5731100/thumb250\"/></a></div>\nTaxonomic
-        treatments have come up in various discussions I''m involved in, and I''m
-        curious as to whether they are actually being used, in particular, whether
-        they are actually being cited. Consider the following quote:\n\n<blockquote>\nThe
-        taxa are described in taxonomic treatments, well defined sections of scientific
-        publications (Catapano 2019). They include a nomenclatural section and one
-        or more sections including descriptions, material citations referring to studied
-        specimens, or notes ecology and behavior. In case the treatment does not describe
-        a new discovered taxon, previous treatments are cited in the form of treatment
-        citations. This citation can refer to a previous treatment and add additional
-        data, or it can be a statement synonymizing the taxon with another taxon.
-        This allows building a citation network, and ultimately is a constituent part
-        of the catalogue of life. - Taxonomic Treatments as Open FAIR Digital Objects
-        <a href=\"https://doi.org/10.3897/rio.8.e93709\">https://doi.org/10.3897/rio.8.e93709</a>\n</blockquote>\n\n<p>\n
-        \"Traditional\" academic citation is from article to article. For example,
-        consider these two papers:\n\n<blockquote>\nLi Y, Li S, Lin Y (2021) Taxonomic
-        study on fourteen symphytognathid species from Asia (Araneae, Symphytognathidae).
-        ZooKeys 1072: 1-47. https://doi.org/10.3897/zookeys.1072.67935\n</blockquote>\n\n<blockquote>\nMiller
-        J, Griswold C, Yin C (2009) The symphytognathoid spiders of the Gaoligongshan,
-        Yunnan, China (Araneae: Araneoidea): Systematics and diversity of micro-orbweavers.
-        ZooKeys 11: 9-195. https://doi.org/10.3897/zookeys.11.160\n</blockquote>\n</p>\n\n<p>Li
-        et al. 2021 cites Miller et al. 2009 (although Pensoft seems to have broken
-        the citation such that it does appear correctly either on their web page or
-        in CrossRef).</p>\n\n<p>So, we have this link: [article]10.3897/zookeys.1072.67935
-        --cites--> [article]10.3897/zookeys.11.160. One article cites another.</p>\n\n<p>In
-        their 2021 paper Li et al. discuss <i>Patu jidanweishi</i> Miller, Griswold
-        & Yin, 2009:\n\n<div class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPavMHXqQNX1ls_zXo9kIcMLHPxc7ZpV9NCSof5wLumrg3ovPoi6nYKzZsINuqFtYoEvW1QrerePD-MEf2DJaYUXlT37d81x3L6ILls7u229rg0_Nc0uUmgW-ICzr6MI_QCZfgQbYGTxuofu-fuPVoygbCnm3vQVYOhLDLtp1EtQ9jRZHDvw/s1040/Screenshot%202022-09-01%20at%2017.12.27.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"314\" data-original-width=\"1040\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPavMHXqQNX1ls_zXo9kIcMLHPxc7ZpV9NCSof5wLumrg3ovPoi6nYKzZsINuqFtYoEvW1QrerePD-MEf2DJaYUXlT37d81x3L6ILls7u229rg0_Nc0uUmgW-ICzr6MI_QCZfgQbYGTxuofu-fuPVoygbCnm3vQVYOhLDLtp1EtQ9jRZHDvw/s400/Screenshot%202022-09-01%20at%2017.12.27.png\"/></a></div>\n\n<p>There
-        is a treatment for the original description of <i>Patu jidanweishi</i> at
-        <a href=\"https://doi.org/10.5281/zenodo.3792232\">https://doi.org/10.5281/zenodo.3792232</a>,
-        which was created by Plazi with a time stamp \"2020-05-06T04:59:53.278684+00:00\".
-        The original publication date was 2009, the treatments are being added retrospectively.</p>\n\n<p>In
-        an ideal world my expectation would be that Li et al. 2021 would have cited
-        the treatment, instead of just providing the text string \"Patu jidanweishi
-        Miller, Griswold & Yin, 2009: 64, figs 65A–E, 66A, B, 67A–D, 68A–F, 69A–F,
-        70A–F and 71A–F (♂♀).\" Isn''t the expectation under the treatment model that
-        we would have seen this relationship:</p>\n\n<p>[article]10.3897/zookeys.1072.67935
-        --cites--> [treatment]https://doi.org/10.5281/zenodo.3792232</p>\n\n<p>Furthermore,
-        if it is the case that \"[i]n case the treatment does not describe a new discovered
-        taxon, previous treatments are cited in the form of treatment citations\"
-        then we should also see a citation between treatments, in other words Li et
-        al.''s 2021 treatment of <i>Patu jidanweishi</i> (which doesn''t seem to have
-        a DOI but is available on Plazi'' web site as <a href=\"https://tb.plazi.org/GgServer/html/1CD9FEC313A35240938EC58ABB858E74\">https://tb.plazi.org/GgServer/html/1CD9FEC313A35240938EC58ABB858E74</a>)
-        should also cite the original treatment? It doesn''t - but it does cite the
-        Miller et al. paper.</p>\n\n<p>So in this example we don''t see articles citing
-        treatments, nor do we see treatments citing treatments. Playing Devil''s advocate,
-        why then do we have treatments? Does''t the lack of citations suggest that
-        - despite some taxonomists saying this is the unit that matters - they actually
-        don''t. If we pay attention to what people do rather than what they say they
-        do, they cite articles.</p>\n\n<p>Now, there are all sorts of reasons why
-        we don''t see [article] -> [treatment] citations, or [treatment] -> [treatment]
-        citations. Treatments are being added after the fact by Plazi, not by the
-        authors of the original work. And in many cases the treatments that could
-        be cited haven''t appeared until after that potentially citing work was published.
-        In the example above the Miller et al. paper dates from 2009, but the treatment
-        extracted only went online in 2020. And while there is a long standing culture
-        of citing publications (ideally using DOIs) there isn''t an equivalent culture
-        of citing treatments (beyond the simple text strings).</p>\n\n<p>Obviously
-        this is but one example. I''d need to do some exploration of the citation
-        graph to get a better sense of citations patterns, perhaps using <a href=\"https://www.crossref.org/documentation/event-data/\">CrossRef''s
-        event data</a>. But my sense is that taxonomists don''t cite treatments.</p>\n\n<p>I''m
-        guessing Plazi would respond by saying treatments are cited, for example (indirectly)
-        in GBIF downloads. This is true, although arguably people aren''t citing the
-        treatment, they''re citing specimen data in those treatments, and that specimen
-        data could be extracted at the level of articles rather than treatments. In
-        other words, it''s not the treatments themselves that people are citing.</p>\n\n<p>To
-        be clear, I think there is value in being able to identify those \"well defined
-        sections\" of a publication that deal with a given taxon (i.e., treatments),
-        but it''s not clear to me that these are actually the citable units people
-        might hope them to be. Likewise, journals such as <i>ZooKeys</i> have DOIs
-        for individual figures. Does anyone actually cite those?</p>","tags":[],"language":"en","references":null},{"id":"https://doi.org/10.59350/en7e9-5s882","uuid":"20b9d31e-513f-496b-b399-4215306e1588","url":"https://iphylo.blogspot.com/2022/04/obsidian-markdown-and-taxonomic-trees.html","title":"Obsidian,
-        markdown, and taxonomic trees","summary":"Returning to the subject of personal
-        knowledge graphs Kyle Scheer has an interesting repository of Markdown files
-        that describe academic disciplines at https://github.com/kyletscheer/academic-disciplines
-        (see his blog post for more background). If you add these files to Obsidian
-        you get a nice visualisation of a taxonomy of academic disciplines. The applications
-        of this to biological taxonomy seem obvious, especially as a tool like Obsidian
-        enables all sorts of interesting links to be added...","date_published":"2022-04-07T21:07:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>Returning to the subject
-        of <a href=\"https://iphylo.blogspot.com/2020/08/personal-knowledge-graphs-obsidian-roam.html\">personal
-        knowledge graphs</a> Kyle Scheer has an interesting repository of Markdown
-        files that describe academic disciplines at <a href=\"https://github.com/kyletscheer/academic-disciplines\">https://github.com/kyletscheer/academic-disciplines</a>
-        (see <a href=\"https://kyletscheer.medium.com/on-creating-a-tree-of-knowledge-f099c1028bf6\">his
-        blog post</a> for more background).</p>\n\n<p>If you add these files to <a
-        href=\"https://obsidian.md/\">Obsidian</a> you get a nice visualisation of
-        a taxonomy of academic disciplines. The applications of this to biological
-        taxonomy seem obvious, especially as a tool like Obsidian enables all sorts
-        of interesting links to be added (e.g., we could add links to the taxonomic
-        research behind each node in the taxonomic tree, the people doing that research,
-        etc. - although that would mean we''d no longer have a simple tree).</p>\n\n<p>The
-        more I look at these sort of simple Markdown-based tools the more I wonder
-        whether we could make more use of them to create simple but persistent databases.
-        Text files seem the most stable, long-lived digital format around, maybe this
-        would be a way to minimise the inevitable obsolescence of database and server
-        software. Time for some experiments I feel... can we take a taxonomic group,
-        such as mammals, and create a richly connected database purely in Markdown?</p>\n\n<div
-        class=\"separator\" style=\"clear: both; text-align: center;\"><iframe allowfullscreen=''allowfullscreen''
-        webkitallowfullscreen=''webkitallowfullscreen'' mozallowfullscreen=''mozallowfullscreen''
-        width=''400'' height=''322'' src=''https://www.blogger.com/video.g?token=AD6v5dy3Sa_SY_MJCZYYCT-bAGe9QD1z_V0tkE0qM5FaQJfAEgGOoHtYPATsNNbBvTEh_tHOZ83nMGzpYRg''
-        class=''b-hbp-video b-uploaded'' frameborder=''0''></iframe></div>","tags":["markdown","obsidian"],"language":"en","references":null},{"id":"https://doi.org/10.59350/m7gb7-d7c49","uuid":"7d814863-43b5-4faf-a475-da8de5efd3ef","url":"https://iphylo.blogspot.com/2022/02/duplicate-dois-again.html","title":"Duplicate
-        DOIs (again)","summary":"This blog post provides some background to a recent
-        tweet where I expressed my frustration about the duplication of DOIs for the
-        same article. I''m going to document the details here. The DOI that alerted
-        me to this problem is https://doi.org/10.2307/2436688 which is for the article
-        Snyder, W. C., & Hansen, H. N. (1940). THE SPECIES CONCEPT IN FUSARIUM. American
-        Journal of Botany, 27(2), 64–67. This article is hosted by JSTOR at https://www.jstor.org/stable/2436688
-        which displays the DOI...","date_published":"2022-02-08T15:06:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>This blog post provides
-        some background to a <a href=\"https://twitter.com/rdmpage/status/1491023036199600132\">recent
-        tweet</a> where I expressed my frustration about the duplication of DOIs for
-        the same article. I''m going to document the details here.</p>\n\n<p>The DOI
-        that alerted me to this problem is <a href=\"https://doi.org/10.2307/2436688\">https://doi.org/10.2307/2436688</a>
-        which is for the article</p>\n\n<blockquote>\nSnyder, W. C., & Hansen, H.
-        N. (1940). THE SPECIES CONCEPT IN FUSARIUM. American Journal of Botany, 27(2),
-        64–67.\n</blockquote>\n\n<p>This article is hosted by JSTOR at <a href=\"https://www.jstor.org/stable/2436688\">https://www.jstor.org/stable/2436688</a>
-        which displays the DOI <a href=\"https://doi.org/10.2307/2436688\">https://doi.org/10.2307/2436688</a>
-        .</p>\n\n<p>This same article is also hosted by Wiley at <a href=\"https://bsapubs.onlinelibrary.wiley.com/doi/abs/10.1002/j.1537-2197.1940.tb14217.x\">https://bsapubs.onlinelibrary.wiley.com/doi/abs/10.1002/j.1537-2197.1940.tb14217.x</a>
-        with the DOI <a href=\"https://doi.org/10.1002/j.1537-2197.1940.tb14217.x\">https://doi.org/10.1002/j.1537-2197.1940.tb14217.x</a>.</p>\n\n<h2>Expected
-        behaviour</h2>\n\n<p>What should happen is if Wiley is going to be the publisher
-        of this content (taking over from JSTOR), the DOI <b>10.2307/2436688</b> should
-        be redirected to the Wiley page, and the Wiley page displays this DOI (i.e.,
-        <b>10.2307/2436688</b>). If I want to get metadata for this DOI, I should
-        be able to use CrossRef''s API to retrieve that metadata, e.g. <a href=\"https://api.crossref.org/v1/works/10.2307/2436688\">https://api.crossref.org/v1/works/10.2307/2436688</a>
-        should return metadata for the article.</p>\n\n<h2>What actually happens</h2>\n\n<p>Wiley
-        display the same article on their web site with the DOI <b>10.1002/j.1537-2197.1940.tb14217.x</b>.
-        They have minted a new DOI for the same article! The original JSTOR DOI now
-        resolves to the Wiley page (you can see this using the <a href=\"https://hdl.handle.net\">Handle
-        Resolver</a>), which is what is supposed to happen. However, Wiley should
-        have reused the original DOI rather than mint their own.</p>\n\n<p>Furthermore,
-        while the original DOI still resolves in a web browser, I can''t retrieve
-        metadata about that DOI from CrossRef, so any attempt to build upon that DOI
-        fails. However, I can retrieve metadata for the Wiley DOI, i.e. <a href=\"https://api.crossref.org/v1/works/10.1002/j.1537-2197.1940.tb14217.x\">https://api.crossref.org/v1/works/10.1002/j.1537-2197.1940.tb14217.x</a>
-        works, but <a href=\"https://api.crossref.org/v1/works/10.2307/2436688\">https://api.crossref.org/v1/works/10.2307/2436688</a>
-        doesn''t.</p>\n\n<h2>Why does this matter?</h2>\n\n<p>For anyone using DOIs
-        as stable links to the literature the persistence of DOIs is something you
-        should be able to rely upon, both for people clicking on links in web browsers
-        and developers getting metadata from those DOIs. The whole rationale of the
-        DOI system is a single, globally unique identifier for each article, and that
-        these DOIs persist even when the publisher of the content changes. If this
-        property doesn''t hold, then why would a developer such as myself invest effort
-        in linking using DOIs?</p>\n\n<p>Just for the record, I think CrossRef is
-        great and is a hugely important part of the scholarly landscape. There are
-        lots of things that I do that would be nearly impossible without CrossRef
-        and its tools. But cases like this where we get massive duplication of DOIs
-        when a publishers takes over an existing journal fundamentally breaks the
-        underlying model of stable, persistent identifiers.</p>","tags":["CrossRef","DOI","duplicates"],"language":"en","references":null},{"id":"https://doi.org/10.59350/d3dc0-7an69","uuid":"545c177f-cea5-4b79-b554-3ccae9c789d7","url":"https://iphylo.blogspot.com/2021/10/reflections-on-macroscope-tool-for-21st.html","title":"Reflections
-        on \"The Macroscope\" - a tool for the 21st Century?","summary":"This is a
-        guest post by Tony Rees. It would be difficult to encounter a scientist, or
-        anyone interested in science, who is not familiar with the microscope, a tool
-        for making objects visible that are otherwise too small to be properly seen
-        by the unaided eye, or to reveal otherwise invisible fine detail in larger
-        objects. A select few with a particular interest in microscopy may also have
-        encountered the Wild-Leica \"Macroscope\", a specialised type of benchtop
-        microscope optimised for...","date_published":"2021-10-07T12:38:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p><img src=\"https://lh3.googleusercontent.com/-A99btr6ERMs/Vl1Wvjp2OtI/AAAAAAAAEFI/7bKdRjNG5w0/ytNkVT2U.jpg?imgmax=800\"
-        alt=\"YtNkVT2U\" title=\"ytNkVT2U.jpg\" border=\"0\" width=\"128\" height=\"128\"
-        style=\"float:right;\" /> This is a guest post by <a href=\"https://about.me/TonyRees\">Tony
-        Rees</a>.</p>\n\n<p>It would be difficult to encounter a scientist, or anyone
-        interested in science, who is not familiar with the microscope, a tool for
-        making objects visible that are otherwise too small to be properly seen by
-        the unaided eye, or to reveal otherwise invisible fine detail in larger objects.
-        A select few with a particular interest in microscopy may also have encountered
-        the Wild-Leica \"Macroscope\", a specialised type of benchtop microscope optimised
-        for low-power macro-photography. However in this overview I discuss the \"Macroscope\"
-        in a different sense, which is that of the antithesis to the microscope: namely
-        a method for visualizing subjects too large to be encompassed by a single
-        field of vision, such as the Earth or some subset of its phenomena (the biosphere,
-        for example), or conceptually, the universe.</p>\n\n<p><div class=\"separator\"
-        style=\"clear: both;\"><a href=\"https://1.bp.blogspot.com/-xXxH9aJn1tY/YV7vnKGQWPI/AAAAAAAAgyQ/7CSJJ663Ry4IXtav54nLcLiI0kda5_L7ACLcBGAsYHQ/s500/2020045672.jpg\"
-        style=\"display: block; padding: 1em 0; text-align: center; clear: right;
-        float: right;\"><img alt=\"\" border=\"0\" height=\"320\" data-original-height=\"500\"
-        data-original-width=\"303\" src=\"https://1.bp.blogspot.com/-xXxH9aJn1tY/YV7vnKGQWPI/AAAAAAAAgyQ/7CSJJ663Ry4IXtav54nLcLiI0kda5_L7ACLcBGAsYHQ/s320/2020045672.jpg\"/></a></div>My
-        introduction to the term was via addresses given by Jesse Ausubel in the formative
-        years of the 2001-2010 <a href=\"http://www.coml.org\">Census of Marine Life</a>,
-        for which he was a key proponent. In Ausubel''s view, the Census would perform
-        the function of a macroscope, permitting a view of everything that lives in
-        the global ocean (or at least, that subset which could realistically be sampled
-        in the time frame available) as opposed to more limited subsets available
-        via previous data collection efforts. My view (which could, of course, be
-        wrong) was that his thinking had been informed by a work entitled \"Le macroscope,
-        vers une vision globale\" published in 1975 by the French thinker Joël de
-        Rosnay, who had expressed such a concept as being globally applicable in many
-        fields, including the physical and natural worlds but also extending to human
-        society, the growth of cities, and more. Yet again, some ecologists may also
-        have encountered the term, sometimes in the guise of \"Odum''s macroscope\",
-        as an approach for obtaining \"big picture\" analyses of macroecological processes
-        suitable for mathematical modelling, typically by elimination of fine detail
-        so that only the larger patterns remain, as initially advocated by Howard
-        T. Odum in his 1971 book \"Environment, Power, and Society\".</p>\n\n<p>From
-        the standpoint of the 21st century, it seems that we are closer to achieving
-        a \"macroscope\" (or possibly, multiple such tools) than ever before, based
-        on the availability of existing and continuing new data streams, improved
-        technology for data assembly and storage, and advanced ways to query and combine
-        these large streams of data to produce new visualizations, data products,
-        and analytical findings. I devote the remainder of this article to examples
-        where either particular workers have employed \"macroscope\" terminology to
-        describe their activities, or where potentially equivalent actions are taking
-        place without the explicit \"macroscope\" association, but are equally worthy
-        of consideration. To save space here, references cited here (most or all)
-        can be found via a Wikipedia article entitled \"<a href=\"https://en.wikipedia.org/wiki/Macroscope_(science_concept)\">Macroscope
-        (science concept)</a>\" that I authored on the subject around a year ago,
-        and have continued to add to on occasion as new thoughts or information come
-        to hand (see <a href=\"https://en.wikipedia.org/w/index.php?title=Macroscope_(science_concept)&offset=&limit=500&action=history\">edit
-        history for the article</a>).</p>\n\n<p>First, one can ask, what constitutes
-        a macroscope, in the present context? In the Wikipedia article I point to
-        a book \"Big Data - Related Technologies, Challenges and Future Prospects\"
-        by Chen <em>et al.</em> (2014) (<a href=\"https://doi.org/10.1007/978-3-319-06245-7\">doi:10.1007/978-3-319-06245-7</a>),
-        in which the \"value chain of big data\" is characterised as divisible into
-        four phases, namely data generation, data acquisition (aka data assembly),
-        data storage, and data analysis. To my mind, data generation (which others
-        may term acquisition, differently from the usage by Chen <em>et al.</em>)
-        is obviously the first step, but does not in itself constitute the macroscope,
-        except in rare cases - such as Landsat imagery, perhaps - where on its own,
-        a single co-ordinated data stream is sufficient to meet the need for a particular
-        type of \"global view\". A variant of this might be a coordinated data collection
-        program - such as that of the ten year Census of Marine Life - which might
-        produce the data required for the desired global view; but again, in reality,
-        such data are collected in a series of discrete chunks, in many and often
-        disparate data formats, and must be \"wrangled\" into a more coherent whole
-        before any meaningful \"macroscope\" functionality becomes available.</p>\n\n<p>Here
-        we come to what, in my view, constitutes the heart of the \"macroscope\":
-        an intelligently organized (i.e. indexable and searchable), coherent data
-        store or repository (where \"data\" may include imagery and other non numeric
-        data forms, but much else besides). Taking the Census of Marine Life example,
-        the data repository for that project''s data (plus other available sources
-        as inputs) is the <a href=\"https://obis.org\">Ocean Biodiversity Information
-        System</a> or OBIS (previously the Ocean Biogeographic Information System),
-        which according to this view forms the \"macroscope\" for which the Census
-        data is a feed. (For non habitat-specific biodiversity data, <a href=\"https://www.gbif.org\">GBIF</a>
-        is an equivalent, and more extensive, operation). Other planetary scale \"macroscopes\",
-        by this definition (which may or may not have an explicit geographic, i.e.
-        spatial, component) would include inventories of biological taxa such as the
-        <a href=\"https://www.catalogueoflife.org\">Catalogue of Life</a> and so on,
-        all the way back to the pioneering compendia published by Linnaeus in the
-        eighteenth century; while for cartography and topographic imagery, the current
-        \"blockbuster\" of <a href=\"http://earth.google.com\">Google Earth</a> and
-        its predecessors also come well into public consciousness.</p>\n\n<p>In the
-        view of some workers and/or operations, both of these phases are precursors
-        to the real \"work\" of the macroscope which is to reveal previously unseen
-        portions of the \"big picture\" by means either of the availability of large,
-        synoptic datasets, or fusion between different data streams to produce novel
-        insights. Companies such as IBM and Microsoft have used phraseology such as:</p>\n\n<blockquote>By
-        2022 we will use machine-learning algorithms and software to help us organize
-        information about the physical world, helping bring the vast and complex data
-        gathered by billions of devices within the range of our vision and understanding.
-        We call this a \"macroscope\" – but unlike the microscope to see the very
-        small, or the telescope that can see far away, it is a system of software
-        and algorithms to bring all of Earth''s complex data together to analyze it
-        by space and time for meaning.\" (IBM)</blockquote>\n\n<blockquote>As the
-        Earth becomes increasingly instrumented with low-cost, high-bandwidth sensors,
-        we will gain a better understanding of our environment via a virtual, distributed
-        whole-Earth \"macroscope\"... Massive-scale data analytics will enable real-time
-        tracking of disease and targeted responses to potential pandemics. Our virtual
-        \"macroscope\" can now be used on ourselves, as well as on our planet.\" (Microsoft)
-        (references available via the Wikipedia article cited above).</blockquote>\n\n<p>Whether
-        or not the analytical capabilities described here are viewed as being an integral
-        part of the \"macroscope\" concept, or are maybe an add-on, is ultimately
-        a question of semantics and perhaps, personal opinion. Continuing the Census
-        of Marine Life/OBIS example, OBIS offers some (arguably rather basic) visualization
-        and summary tools, but also makes its data available for download to users
-        wishing to analyse it further according to their own particular interests;
-        using OBIS data in this manner, Mark Costello et al. in 2017 were able to
-        demarcate a finite number of data-supported marine biogeographic realms for
-        the first time (Costello et al. 2017: Nature Communications. 8: 1057. <a href=\"https://doi.org/10.1038/s41467-017-01121-2\">doi:10.1038/s41467-017-01121-2</a>),
-        a project which I was able to assist in a small way in an advisory capacity.
-        In a case such as this, perhaps the final function of the macroscope, namely
-        data visualization and analysis, was outsourced to the authors'' own research
-        institution. Similarly at an earlier phase, \"data aggregation\" can also
-        be virtual rather than actual, i.e. avoiding using a single physical system
-        to hold all the data, enabled by open web mapping standards WMS (web map service)
-        and WFS (web feature service) to access a set of distributed data stores,
-        e.g. as implemented on the portal for the <a href=\"https://portal.aodn.org.au/\">Australian
-        Ocean Data Network</a>.</p>\n\n<p>So, as we pass through the third decade
-        of the twenty first century, what developments await us in the \"macroscope\"
-        area\"? In the biodiversity space, one can reasonably presume that the existing
-        \"macroscopic\" data assembly projects such as OBIS and GBIF will continue,
-        and hopefully slowly fill current gaps in their coverage - although in the
-        marine area, strategic new data collection exercises may be required (Census
-        2020, or 2025, anyone?), while (again hopefully), the Catalogue of Life will
-        continue its progress towards a \"complete\" species inventory for the biosphere.
-        The Landsat project, with imagery dating back to 1972, continues with the
-        launch of its latest satellite Landsat 9 just this year (21 September 2021)
-        with a planned mission duration for the next 5 years, so the \"macroscope\"
-        functionality of that project seems set to continue for the medium term at
-        least. Meanwhile the ongoing development of sensor networks, both on land
-        and in the ocean, offers an exciting new method of \"instrumenting the earth\"
-        to obtain much more real time data than has ever been available in the past,
-        offering scope for many more, use case-specific \"macroscopes\" to be constructed
-        that can fuse (e.g.) satellite imagery with much more that is happening at
-        a local level.</p>\n\n<p>So, the \"macroscope\" concept appears to be alive
-        and well, even though the nomenclature can change from time to time (IBM''s
-        \"Macroscope\", foreshadowed in 2017, became the \"IBM Pairs Geoscope\" on
-        implementation, and is now simply the \"Geospatial Analytics component within
-        the IBM Environmental Intelligence Suite\" according to available IBM publicity
-        materials). In reality this illustrates a new dichotomy: even if \"everyone\"
-        in principle has access to huge quantities of publicly available data, maybe
-        only a few well funded entities now have the computational ability to make
-        sense of it, and can charge clients a good fee for their services...</p>\n\n<p>I
-        present this account partly to give a brief picture of \"macroscope\" concepts
-        today and in the past, for those who may be interested, and partly to present
-        a few personal views which would be out of scope in a \"neutral point of view\"
-        article such as is required on Wikipedia; also to see if readers of this blog
-        would like to contribute further to discussion of any of the concepts traversed
-        herein.</p>","tags":["guest post","macroscope"],"language":"en","references":null},{"id":"https://doi.org/10.59350/2b1j9-qmw12","uuid":"37538c38-66e6-4ac4-ab5c-679684622ade","url":"https://iphylo.blogspot.com/2022/05/round-trip-from-identifiers-to.html","title":"Round
-        trip from identifiers to citations and back again","summary":"Note to self
-        (basically rewriting last year''s Finding citations of specimens). Bibliographic
-        data supports going from identifier to citation string and back again, so
-        we can do a \"round trip.\" 1. Given a DOI we can get structured data with
-        a simple HTTP fetch, then use a tool such as citation.js to convert that data
-        into a human-readable string in a variety of formats. Identifier ⟶ Structured
-        data ⟶ Human readable string 10.7717/peerj-cs.214 HTTP with...","date_published":"2022-05-27T16:34:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>Note to self (basically
-        rewriting last year''s <a href=\"https://iphylo.blogspot.com/2021/05/finding-citations-of-specimens.html\">Finding
-        citations of specimens</a>).</p>\n\n<p>Bibliographic data supports going from
-        identifier to citation string and back again, so we can do a \"round trip.\"</p>\n\n<h2>1.</h2>\n\n<p>Given
-        a DOI we can get structured data with a simple HTTP fetch, then use a tool
-        such as <a href=\"https://citation.js.org\">citation.js</a> to convert that
-        data into a human-readable string in a variety of formats.</p>\n\n<table>\n<tr>\n<th>\nIdentifier\n</th>\n<th>\n⟶\n</th>\n<th>\nStructured
-        data\n</th>\n<th>\n⟶\n</th>\n<th>\nHuman readable string\n</th>\n<tr>\n<tr>\n<td>\n10.7717/peerj-cs.214\n</td>\n<td>\nHTTP
-        with content-negotiation\n</td>\n<td>\nCSL-JSON\n</td>\n<td>\nCSL templates\n</td>\n<td
-        width=\"25%\">\nWillighagen, L. G. (2019). Citation.js: a format-independent,
-        modular bibliography tool for the browser and command line. PeerJ Computer
-        Science, 5, e214. https://doi.org/10.7717/peerj-cs.214\n</td>\n</tr>\n</table>\n\n<h2>2.</h2>\n\n<p>Going
-        in the reverse direction (string to identifier) is a little more challenging.
-        In the \"old days\" a typical strategy was to attempt to parse the citation
-        string into structured data (see <a href=\"hhtps://anystyle.io\">AnyStyle</a>
-        for a nice example of this), then we could extract a truple of (journal, volume,
-        starting page) and use that to query CrossRef to find if there was an article
-        with that tuple, which gave us the DOI.</p>\n\n<table>\n<tr>\n<th>\nIdentifier\n</th>\n<th>\n⟵\n</th>\n<th>\nStructured
-        data\n</th>\n<th>\n⟵\n</th>\n<th>\nHuman readable string\n</th>\n<tr>\n<tr>\n<td>\n10.7717/peerj-cs.214\n</td>\n<td>\nOpenURL
-        query\n</td>\n<td>\njournal, volume, start page\n</td>\n<td>\nCitation parser
-        \n</td>\n<td width=\"25%\">\nWillighagen, L. G. (2019). Citation.js: a format-independent,
-        modular bibliography tool for the browser and command line. PeerJ Computer
-        Science, 5, e214. https://doi.org/10.7717/peerj-cs.214\n</td>\n</tr>\n</table>\n\n<h2>3.</h2>\n\n<p>Another
-        strategy is to take all the citations strings for each DOI, index those in
-        a search engine, then just use a simple search to find the best match to your
-        citation string, and hence the DOI. This is what <a href=\"https://search.crossref.org\">https://search.crossref.org</a>
-        does.</p>\n\n<table>\n<tr>\n<th>\nIdentifier\n</th>\n<th>\n⟵\n</th>\n<th>\nHuman
-        readable string\n</th>\n<tr>\n<tr>\n<td>\n10.7717/peerj-cs.214\n</td>\n<td>\nsearch\n</td>\n<td
-        width=\"50%\">\nWillighagen, L. G. (2019). Citation.js: a format-independent,
-        modular bibliography tool for the browser and command line. PeerJ Computer
-        Science, 5, e214. https://doi.org/10.7717/peerj-cs.214\n</td>\n</tr>\n</table>\n\n<p>At
-        the moment my work on material citations (i.e., lists of specimens in taxonomic
-        papers) is focussing on 1 (generating citations from specimen data in GBIF)
-        and 2 (parsing citations into structured data).</p>","tags":["citation","GBIF","material
-        examined","specimen codes"],"language":"en","references":null},{"id":"https://doi.org/10.59350/3s376-6bm21","uuid":"62e7b438-67a3-44ac-a66d-3f5c278c949e","url":"https://iphylo.blogspot.com/2022/02/deduplicating-bibliographic-data.html","title":"Deduplicating
+        list can be modelled in RDF in...","published_at":1630070400,"updated_at":1630070987,"indexed_at":1688982503,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["JSON-LD","RDF"],"language":"en","reference":[]},{"id":"5891c709-d139-440f-bacb-06244424587a","doi":"https://doi.org/10.59350/pmhat-5ky65","url":"https://iphylo.blogspot.com/2021/10/problems-with-plazi-parsing-how.html","title":"Problems
+        with Plazi parsing: how reliable are automated methods for extracting specimens
+        from the literature?","summary":"The Plazi project has become one of the major
+        contributors to GBIF with some 36,000 datasets yielding some 500,000 occurrences
+        (see Plazi''s GBIF page for details). These occurrences are extracted from
+        taxonomic publication using automated methods. New data is published almost
+        daily (see latest treatments). The map below shows the geographic distribution
+        of material citations provided to GBIF by Plazi, which gives you a sense of
+        the size of the dataset. By any metric Plazi represents a...","published_at":1635160200,"updated_at":1635437298,"indexed_at":1688982503,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["data quality","parsing","Plazi","specimen","text
+        mining"],"language":"en","reference":[]},{"id":"3cb94422-5506-4e24-a41c-a250bb521ee0","doi":"https://doi.org/10.59350/c79vq-7rr11","url":"https://iphylo.blogspot.com/2021/12/graphql-for-wikidata-wikicite.html","title":"GraphQL
+        for WikiData (WikiCite)","summary":"I''ve released a very crude GraphQL endpoint
+        for WikiData. More precisely, the endpoint is for a subset of the entities
+        that are of interest to WikiCite, such as scholarly articles, people, and
+        journals. There is a crude demo at https://wikicite-graphql.herokuapp.com.
+        The endpoint itself is at https://wikicite-graphql.herokuapp.com/gql.php.
+        There are various ways to interact with the endpoint, personally I like the
+        Altair GraphQL Client by Samuel Imolorhe. As I''ve mentioned earlier it''s
+        taken...","published_at":1640006160,"updated_at":1640006405,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["GraphQL","SPARQL","WikiCite","Wikidata"],"language":"en","reference":[]},{"id":"62e7b438-67a3-44ac-a66d-3f5c278c949e","doi":"https://doi.org/10.59350/3s376-6bm21","url":"https://iphylo.blogspot.com/2022/02/deduplicating-bibliographic-data.html","title":"Deduplicating
         bibliographic data","summary":"There are several instances where I have a
         collection of references that I want to deduplicate and merge. For example,
         in Zootaxa has no impact factor I describe a dataset of the literature cited
         by articles in the journal Zootaxa. This data is available on Figshare (https://doi.org/10.6084/m9.figshare.c.5054372.v4),
         as is the equivalent dataset for Phytotaxa (https://doi.org/10.6084/m9.figshare.c.5525901.v1).
         Given that the same articles may be cited many times, these datasets have
-        lots of...","date_published":"2022-02-03T15:09:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>There are several instances
-        where I have a collection of references that I want to deduplicate and merge.
-        For example, in <a href=\"https://iphylo.blogspot.com/2020/07/zootaxa-has-no-impact-factor.html\">Zootaxa
-        has no impact factor</a> I describe a dataset of the literature cited by articles
-        in the journal <i>Zootaxa</i>. This data is available on Figshare (<a href=\"https://doi.org/10.6084/m9.figshare.c.5054372.v4\">https://doi.org/10.6084/m9.figshare.c.5054372.v4</a>),
-        as is the equivalent dataset for <i>Phytotaxa</i> (<a href=\"https://doi.org/10.6084/m9.figshare.c.5525901.v1\">https://doi.org/10.6084/m9.figshare.c.5525901.v1</a>).
-        Given that the same articles may be cited many times, these datasets have
-        lots of duplicates. Similarly, articles in <a href=\"https://species.wikimedia.org\">Wikispecies</a>
-        often have extensive lists of references cited, and the same reference may
-        appear on multiple pages (for an initial attempt to extract these references
-        see <a href=\"https://doi.org/10.5281/zenodo.5801661\">https://doi.org/10.5281/zenodo.5801661</a>
-        and <a href=\"https://github.com/rdmpage/wikispecies-parser\">https://github.com/rdmpage/wikispecies-parser</a>).</p>\n\n<p>There
-        are several reasons I want to merge these references. If I want to build a
-        citation graph for <i>Zootaxa</i> or <i>Phytotaxa</i> I need to merge references
-        that are the same so that I can accurate count citations. I am also interested
-        in harvesting the metadata to help find those articles in the <a href=\"https://www.biodiversitylibrary.org\">Biodiversity
-        Heritage Library</a> (BHL), and the literature cited section of scientific
-        articles is a potential goldmine of bibliographic metadata, as is Wikispecies.</p>\n\n<p>After
-        various experiments and false starts I''ve created a repository <a href=\"https://github.com/rdmpage/bib-dedup\">https://github.com/rdmpage/bib-dedup</a>
-        to host a series of PHP scripts to deduplicate bibliographics data. I''ve
-        settled on using CSL-JSON as the format for bibliographic data. Because deduplication
-        relies on comparing pairs of references, the standard format for most of the
-        scripts is a JSON array containing a pair of CSL-JSON objects to compare.
-        Below are the steps the code takes.</p>\n\n<h2>Generating pairs to compare</h2>\n\n<p>The
-        first step is to take a list of references and generate the pairs that will
-        be compared. I started with this approach as I wanted to explore machine learning
-        and wanted a simple format for training data, such as an array of two CSL-JSON
-        objects and an integer flag representing whether the two references were the
-        same of different.</p>\n\n<p>There are various ways to generate CSL-JSON for
-        a reference. I use a tool I wrote (see <a href=\"https://iphylo.blogspot.com/2021/07/citation-parsing-released.html\">Citation
-        parsing tool released</a>) that has a simple API where you parse one or more
-        references and it returns that reference as structured data in CSL-JSON.</p>\n\n<p>Attempting
-        to do all possible pairwise comparisons rapidly gets impractical as the number
-        of references increases, so we need some way to restrict the number of comparisons
-        we make. One approach I''ve explored is the “sorted neighbourhood method”
-        where we sort the references 9for example by their title) then move a sliding
-        window down the list of references, comparing all references within that window.
-        This greatly reduces the number of pairwise comparisons. So the first step
-        is to sort the references, then run a sliding window over them, output all
-        the pairs in each window (ignoring in pairwise comparisons already made in
-        a previous window). Other methods of \"blocking\" could also be used, such
-        as only including references in a particular year, or a particular journal.</p>\n\n<p>So,
-        the output of this step is a set of JSON arrays, each with a pair of references
-        in CSL-JSON format. Each array is stored on a single line in the same file
-        in <a href=\"https://en.wikipedia.org/wiki/JSON_streaming#Line-delimited_JSON_2\">line-delimited
-        JSON</a> (JSONL).</p>\n\n<h2>Comparing pairs</h2>\n\n<p>The next step is to
-        compare each pair of references and decide whether they are a match or not.
-        Initially I explored a machine learning approach used in the following paper:</p>\n\n<blockquote>\nWilson
-        DR. 2011. Beyond probabilistic record linkage: Using neural networks and complex
-        features to improve genealogical record linkage. In: The 2011 International
-        Joint Conference on Neural Networks. 9–14. DOI: <a href=\"https://doi.org/10.1109/IJCNN.2011.6033192\">10.1109/IJCNN.2011.6033192</a>\n</blockquote>\n\n<p>Initial
-        experiments using <a href=\"https://github.com/jtet/Perceptron\">https://github.com/jtet/Perceptron</a>
-        were promising and I want to play with this further, but I deciding to skip
-        this for now and just use simple string comparison. So for each CSL-JSON object
-        I generate a citation string in the same format using CiteProc, then compute
-        the <a href=\"https://en.wikipedia.org/wiki/Levenshtein_distance\">Levenshtein
-        distance</a> between the two strings. By normalising this distance by the
-        length of the two strings being compared I can use an arbitrary threshold
-        to decide if the references are the same or not.</p>\n\n<h2>Clustering</h2>\n\n<p>For
-        this step we read the JSONL file produced above and record whether the two
-        references are a match or not. Assuming each reference has a unique identifier
-        (needs only be unique within the file) then we can use those identifier to
-        record the clusters each reference belongs to. I do this using a <a href=\"https://en.wikipedia.org/wiki/Disjoint-set_data_structure\">Disjoint-set
-        data structure</a>. For each reference start with a graph where each node
-        represents a reference, and each node has a pointer to a parent node. Initially
-        the reference is its own parent. A simple implementation is to have an array
-        index by reference identifiers and where the value of each cell in the array
-        is the node''s parent.</p>\n\n<p>As we discover pairs we update the parents
-        of the nodes to reflect this, such that once all the comparisons are done
-        we have a one or more sets of clusters corresponding to the references that
-        we think are the same. Another way to think of this is that we are getting
-        the components of a graph where each node is a reference and pair of references
-        that match are connected by an edge.</p>\n\n<p>In the code I''m using I write
-        this graph in <a href=\"https://en.wikipedia.org/wiki/Trivial_Graph_Format\">Trivial
-        Graph Format</a> (TGF) which can be visualised using a tools such as <a href=\"https://www.yworks.com/products/yed\">yEd</a>.</p>\n\n<h2>Merging</h2>\n\n<p>Now
-        that we have a graph representing the sets of references that we think are
-        the same we need to merge them. This is where things get interesting as the
-        references are similar (by definition) but may differ in some details. The
-        paper below describes a simple Bayesian approach for merging records:</p>\n\n<blockquote>\nCouncill
-        IG, Li H, Zhuang Z, Debnath S, Bolelli L, Lee WC, Sivasubramaniam A, Giles
-        CL. 2006. Learning Metadata from the Evidence in an On-line Citation Matching
-        Scheme. In: Proceedings of the 6th ACM/IEEE-CS Joint Conference on Digital
-        Libraries. JCDL ’06. New York, NY, USA: ACM, 276–285. DOI: <a href=\"https://doi.org/10.1145/1141753.1141817\">10.1145/1141753.1141817</a>.\n</blockquote>\n\n<p>So
-        the next step is to read the graph with the clusters, generate the sets of
-        bibliographic references that correspond to each cluster, then use the method
-        described in Councill et al. to produce a single bibliographic record for
-        that cluster. These records could then be used to, say locate the corresponding
-        article in BHL, or populate Wikidata with missing references.</p>\n\n<p>Obviously
-        there is always the potential for errors, such as trying to merge references
-        that are not the same. As a quick and dirty check I flag as dubious any cluster
-        where the page numbers vary among members of the cluster. More sophisticated
-        checks are possible, especially if I go down the ML route (i.e., I would have
-        evidence for the probability that the same reference can disagree on some
-        aspects of metadata).</p>\n\n<h2>Summary</h2>\n\n<p>At this stage the code
-        is working well enough for me to play with and explore some example datasets.
-        The focus is on structured bibliographic metadata, but I may simplify things
-        and have a version that handles simple string matching, for example to cluster
-        together different abbreviations of the same journal name.</p>","tags":["data
-        cleaning","deduplication","Phytotaxa","Wikispecies","Zootaxa"],"language":"en","references":null},{"id":"https://doi.org/10.59350/ndtkv-6ve80","uuid":"e8e95aaf-bacb-4b5a-bf91-54e903526ab2","url":"https://iphylo.blogspot.com/2021/11/revisiting-rss-to-monitor-latests.html","title":"Revisiting
+        lots of...","published_at":1643900940,"updated_at":1643901089,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["data cleaning","deduplication","Phytotaxa","Wikispecies","Zootaxa"],"language":"en","reference":[]},{"id":"d33d4f49-b281-4997-9eb9-dbad1e52d9bd","doi":"https://doi.org/10.59350/92rdb-5fe58","url":"https://iphylo.blogspot.com/2022/09/local-global-identifiers-for.html","title":"Local
+        global identifiers for decentralised wikis","summary":"I''ve been thinking
+        a bit about how one could use a Markdown wiki-like tool such as Obsidian to
+        work with taxonomic data (see earlier posts Obsidian, markdown, and taxonomic
+        trees and Personal knowledge graphs: Obsidian, Roam, Wikidata, and Xanadu).
+        One \"gotcha\" would be how to name pages. If we treat the database as entirely
+        local, then the page names don''t matter, but what if we envisage sharing
+        the database, or merging it with others (for example, if we divided a taxon
+        up into chunks, and...","published_at":1662653340,"updated_at":1662657862,"indexed_at":1688982864,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["citekey","identfiiers","markdown","obsidian","Roger
+        Hyam"],"language":"en","reference":[]},{"id":"6a4d5c44-f4a9-4d40-a32c-a4d5e512c55a","doi":"https://doi.org/10.59350/rfxj3-x6739","url":"https://iphylo.blogspot.com/2022/05/thoughts-on-treebase-dying.html","title":"Thoughts
+        on TreeBASE dying(?)","summary":"@rvosa is Naturalis no longer hosting Treebase?
+        https://t.co/MBRgcxaBmR— Hilmar Lapp (@hlapp) May 10, 2022 So it looks like
+        TreeBASE is in trouble, it''s legacy Java code a victim of security issues.
+        Perhaps this is a chance to rethink TreeBASE, assuming that a repository of
+        published phylogenies is still considered a worthwhile thing to have (and
+        I think that question is open). Here''s what I think could be done. The data
+        (individual studies with trees and data) are packaged into...","published_at":1652287980,"updated_at":1652350205,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["phylogeny","TreeBASE"],"language":"en","reference":[]},{"id":"3e1278f6-e7c0-43e1-bb54-6829e1344c0d","doi":"https://doi.org/10.59350/btdk4-42879","url":"https://iphylo.blogspot.com/2022/09/the-ideal-taxonomic-journal.html","title":"The
+        ideal taxonomic journal","summary":"This is just some random notes on an “ideal”
+        taxonomic journal, inspired in part by some recent discussions on “turbo-taxonomy”
+        (e.g., https://doi.org/10.3897/zookeys.1087.76720 and https://doi.org/10.1186/1742-9994-10-15),
+        and also examples such as the Australian Journal of Taxonomy https://doi.org/10.54102/ajt.qxi3r
+        which seems well-intentioned but limited. XML One approach is to have highly
+        structured text that embeds detailed markup, and ideally a tool that generates
+        markup in XML. This is...","published_at":1664460000,"updated_at":1664460001,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":[],"language":"en","reference":[]},{"id":"a93134aa-8b33-4dc7-8cd4-76cdf64732f4","doi":"https://doi.org/10.59350/cbzgz-p8428","url":"https://iphylo.blogspot.com/2023/04/library-interfaces-knowledge-graphs-and.html","title":"Library
+        interfaces, knowledge graphs, and Miller columns","summary":"Some quick notes
+        on interface ideas for digital libraries and/or knowledge graphs. Recently
+        there’s been something of an explosion in bibliographic tools to explore the
+        literature. Examples include: Elicit which uses AI to search for and summarise
+        papers _scite which uses AI to do sentiment analysis on citations (does paper
+        A cite paper B favourably or not?) ResearchRabbit which uses lists, networks,
+        and timelines to discover related research Scispace which navigates connections
+        between...","published_at":1682427660,"updated_at":1682607068,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["cards","flow","Knowledge Graph","Miller column","RabbitResearch"],"language":"en","reference":[]},{"id":"dc829ab3-f0f1-40a4-b16d-a36dc0e34166","doi":"https://doi.org/10.59350/463yw-pbj26","url":"https://iphylo.blogspot.com/2022/12/david-remsen.html","title":"David
+        Remsen","summary":"I heard yesterday from Martin Kalfatovic (BHL) that David
+        Remsen has died. Very sad news. It''s starting to feel like iPhylo might end
+        up being a list of obituaries of people working on biodiversity informatics
+        (e.g., Scott Federhen). I spent several happy visits at MBL at Woods Hole
+        talking to Dave at the height of the uBio project, which really kickstarted
+        large scale indexing of taxonomic names, and the use of taxonomic name finding
+        tools to index the literature. His work on uBio with David...","published_at":1671213240,"updated_at":1671264743,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["David Remsen","obituary","uBio"],"language":"en","reference":[]},{"id":"30c78d9d-2e50-49db-9f4f-b3baa060387b","doi":"https://doi.org/10.59350/zc4qc-77616","url":"https://iphylo.blogspot.com/2022/09/does-anyone-cite-taxonomic-treatments.html","title":"Does
+        anyone cite taxonomic treatments?","summary":"Taxonomic treatments have come
+        up in various discussions I''m involved in, and I''m curious as to whether
+        they are actually being used, in particular, whether they are actually being
+        cited. Consider the following quote: The taxa are described in taxonomic treatments,
+        well defined sections of scientific publications (Catapano 2019). They include
+        a nomenclatural section and one or more sections including descriptions, material
+        citations referring to studied specimens, or notes ecology and...","published_at":1662050940,"updated_at":1662050991,"indexed_at":1688982503,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":[],"language":"en","reference":[]},{"id":"c6b101f4-bfbc-4d01-921d-805c43c85757","doi":"https://doi.org/10.59350/j77nc-e8x98","url":"https://iphylo.blogspot.com/2022/08/linking-taxonomic-names-to-literature.html","title":"Linking
+        taxonomic names to the literature","summary":"Just some thoughts as I work
+        through some datasets linking taxonomic names to the literature. In the diagram
+        above I''ve tried to capture the different situatios I encounter. Much of
+        the work I''ve done on this has focussed on case 1 in the diagram: I want
+        to link a taxonomic name to an identifier for the work in which that name
+        was published. In practise this means linking names to DOIs. This has the
+        advantage of linking to a citable indentifier, raising questions such as whether
+        citations...","published_at":1661188740,"updated_at":1661188748,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":[],"language":"en","reference":[]},{"id":"e8e95aaf-bacb-4b5a-bf91-54e903526ab2","doi":"https://doi.org/10.59350/ndtkv-6ve80","url":"https://iphylo.blogspot.com/2021/11/revisiting-rss-to-monitor-latests.html","title":"Revisiting
         RSS to monitor the latest taxonomic research","summary":"Over a decade ago
         RSS (RDF Site Summary or Really Simple Syndication) was attracting a lot of
         interest as a way to integrate data across various websites. Many science
@@ -1210,206 +197,45 @@ http_interactions:
         three flavours of RSS (RDF, RSS, Atom). This led to tools such as uBioRSS
         [1] and my own e-Biosphere Challenge: visualising biodiversity digitisation
         in real time. It was a time of enthusiasm for aggregating lots of data, such
-        as the ill-fated PLoS...","date_published":"2021-11-23T20:53:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<div class=\"separator\" style=\"clear:
-        both;\"><a href=\"https://1.bp.blogspot.com/-dsij6_nhdsc/SgHYU5MCwsI/AAAAAAAAAe8/9KN6Gm87sj0PCuJG-crvZoMbL8MJvusegCPcBGAYYCw/s257/feedicon.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; clear: right;
-        float: right;\"><img alt=\"\" border=\"0\" width=\"128\" data-original-height=\"257\"
-        data-original-width=\"257\" src=\"https://1.bp.blogspot.com/-dsij6_nhdsc/SgHYU5MCwsI/AAAAAAAAAe8/9KN6Gm87sj0PCuJG-crvZoMbL8MJvusegCPcBGAYYCw/s200/feedicon.png\"/></a></div>\n<p>Over
-        a decade ago <a href=\"https://en.wikipedia.org/wiki/RSS\">RSS</a> (RDF Site
-        Summary or Really Simple Syndication) was attracting a lot of interest as
-        a way to integrate data across various websites. Many science publishers would
-        provide a list of their latest articles in XML in one of three flavours of
-        RSS (RDF, RSS, Atom). This led to tools such as <a href=\"http://ubio.org/rss/\">uBioRSS</a>
-        [<a href=\"#Leary2007\">1</a>] and my own <a href=\"https://iphylo.blogspot.com/2009/05/e-biosphere-challenge-visualising.html\">e-Biosphere
-        Challenge: visualising biodiversity digitisation in real time</a>. It was
-        a time of enthusiasm for aggregating lots of data, such as the <a href=\"https://iphylo.blogspot.com/2013/07/the-demise-of-plos-biodiversity-hub.html\">ill-fated</a>
-        PLoS Biodiversity Hub [<a href=\"#Mindell2011\">2</a>].</p>\n\n<p>Since I
-        seem to be condemned to revisit old ideas rather than come up with anything
-        new,  I''ve been looking at providing a tool like the now defunct uBioRSS.
-        The idea is to harvest RSS feeds from journals (with an emphasis on taxonomic
-        and systematic journals), aggregate the results, and make them browsable by
-        taxon and geography. Here''s a sneak peak:</p>\n\n<div class=\"separator\"
-        style=\"clear: both;\"><a href=\"https://1.bp.blogspot.com/-toYkBpS81tE/YZ1VY1DU1FI/AAAAAAAAg4E/yFMM4Xc3AEE8BjCj0jKO0sLtT9ZI-3k8ACLcBGAsYHQ/s1032/Screenshot%2B2021-11-23%2Bat%2B20.00.06.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"952\" data-original-width=\"1032\"
-        src=\"https://1.bp.blogspot.com/-toYkBpS81tE/YZ1VY1DU1FI/AAAAAAAAg4E/yFMM4Xc3AEE8BjCj0jKO0sLtT9ZI-3k8ACLcBGAsYHQ/s400/Screenshot%2B2021-11-23%2Bat%2B20.00.06.png\"/></a></div>\n\n<p>What
-        seems like a straightforward task quickly became a bit of a challenge. Not
-        all journals have RSS feeds (they seem to have become less widely supported
-        over time) so I need to think of alternative ways to get lists of recent articles.
-        These lists also need to be processed in various ways. There are three versions
-        of RSS, each with their own idiosyncracies, so I need to standardise things
-        like dates. I also want to augment them with things like DOIs (often missing
-        from RSS feeds) and thumbnails for the articles (often available on publisher
-        websites but not the feeds). Then I need to index the content by taxon and
-        geography. For taxa I use a version of Patrick Leary''s \"taxonfinder\" (see
-        <a href=\"https://right-frill.glitch.me\">https://right-frill.glitch.me</a>)
-        to find names, then the <a href=\"https://index.globalnames.org\">Global Names
-        Index</a> to assign names found to the GBIF taxonomic hierarchy.</p>\n\n<p>Indexing
-        by geography proved harder. Typically <a href=\"https://en.wikipedia.org/wiki/Toponym_resolution#Geoparsing\">geoparsing</a>
-        involves taking a body of text and doing the following:\n<ul><li>Using named-entity
-        recognition <a href=\"https://en.wikipedia.org/wiki/Named-entity_recognition\">NER</a>
-        to identity named entities in the text (e.g., place names, people names, etc.).</li>\n<li>Using
-        a gazetteer of geographic names <a href=\"http://www.geonames.org\">GeoNames</a>
-        to try and match the place names found by NER.</li>\n</ul></p>\n\n<p>An example
-        of such a parser is the <a href=\"https://www.ltg.ed.ac.uk/software/geoparser/\">Edinburgh
-        Geoparser</a>. Typically geoparsing software can be large and tricky to install,
-        especially if you are looking to make your installation publicly accessible.
-        Geoparsing services seem to have a short half-life (e.g., <a href=\"https://geoparser.io\">Geoparser.io</a>),
-        perhaps because they are so useful they quickly get swamped by users.</p>\n\n<p>Bearing
-        this in mind, the approach I’ve taken here is to create a very simple geoparser
-        that is focussed on fairly large areas, especially those relevant to biodiversity,
-        and is aimed at geoparsing text such as abstracts of scientific papers. I''ve
-        created a small database of places by harvesting data from Wikidata, then
-        I use the \"flash text\" algorithm [<a href=\"#Singh2017\">3</a>] to find
-        geographic places. This approach uses a <a href=\"https://en.wikipedia.org/wiki/Trie\">trie</a>
-        to store the place names. All I do is walk through the text seeing whether
-        the current word matches a place name (or the start of one) in the trie, then
-        moving on. This is very quick and seems to work quite well.</p>\n\n<p>Given
-        that I need to aggregate data from a lot of sources, apply various transformations
-        to that data, then merge it, there are a lot of moving parts. I started playing
-        with a \"NoCode\" platform for creating workflows, in this case <a href=\"https://n8n.io\">n8n</a>
-        (in many ways reminiscent of the now defunct <a href=\"https://en.wikipedia.org/wiki/Yahoo!_Pipes\">Yahoo
-        Pipes</a>). This was quite fun for a while, but after lots of experimentation
-        I moved back to writing code to aggregate the data into a CouchDB database.
-        CouchDB is one of the NoSQL databases that I really like as it has a great
-        interface, and makes queries very easy to do once you get your head around
-        how it works.</p>\n\n<p>So the end result of this is \"BioRSS\" <a href=\"https://biorss.herokuapp.com\">https://biorss.herokuapp.com</a>.
-        The interface comprises a stream of articles listed from newest to oldest,
-        with a treemap and a geographic map on the left. You can use these to filter
-        the articles by taxonomic group and/or country. For example the screen shot
-        is showing arthropods from China (in this case from a month or two ago in
-        the journal <i>ZooKeys</i>). As much fun as the interface has been to construct,
-        in many ways I don''t really want to spend time making an interface. For each
-        combination of taxon and country I provide a RSS feed so if you have a favour
-        feed reader you can grab the feed and view it there. As BioRSS updates the
-        data your feed reader should automatically update the feed. This means that
-        you can have a feed that monitors, say, new papers on spiders in China.</p>\n\n<p>In
-        the spirit of \"release early and release often\" this is an early version
-        of this app. I need to add a lot more feeds, back date them to bring in older
-        content, and I also want to make use of aggregators such as PubMed, CrossRef,
-        and Google Scholar. The existence of these tools is, I suspect, one reason
-        why RSS feeds are less common than they used to be.</p>\n\n<p>So, if this
-        sounds useful please take it for a spin at <a href=\"https://biorss.herokuapp.com\">https://biorss.herokuapp.com</a>.
-        Feedback is welcome, especially suggestions for journals to harvest and add
-        to the news feed. Ultimately I''d like to have sufficient coverage of the
-        taxonomic literature so that BioRSS becomes a place where we can go to find
-        the latest papers on any taxon of interest.</p>\n\n<h2>References</h2>\n\n<blockquote>\n<a
-        name=\"Leary2007\">1.</a> Patrick R. Leary, David P. Remsen, Catherine N.
-        Norton, David J. Patterson, Indra Neil Sarkar, uBioRSS: Tracking taxonomic
-        literature using RSS, Bioinformatics, Volume 23, Issue 11, June 2007, Pages
-        1434–1436, <a href=\"https://doi.org/10.1093/bioinformatics/btm109\">https://doi.org/10.1093/bioinformatics/btm109</a>\n</blockquote>\n\n<blockquote><a
-        name=\"Mindell2011\">2.</a> Mindell, D. P., Fisher, B. L., Roopnarine, P.,
-        Eisen, J., Mace, G. M., Page, R. D. M., & Pyle, R. L. (2011). Aggregating,
-        Tagging and Integrating Biodiversity Research. PLoS ONE, 6(8), e19491. <a
-        href=\"https://doi.org/10.1371/journal.pone.0019491\">doi:10.1371/journal.pone.0019491</a>\n</blockquote>\n\n<blockquote><a
-        name=\"Singh2017\">3.</a> Singh, V. (2017). Replace or Retrieve Keywords In
-        Documents at Scale. CoRR, abs/1711.00046. <a href=\"http://arxiv.org/abs/1711.00046\">http://arxiv.org/abs/1711.00046</a>\n\n</blockquote>","tags":["geocoding","NoCode","RSS"],"language":"en","references":[{"doi":"https://doi.org/10.1093/bioinformatics/btm109","key":"ref1"},{"doi":"https://doi.org/10.1371/journal.pone.0019491","key":"ref2"},{"key":"ref3","url":"http://arxiv.org/abs/1711.00046"}]},{"id":"https://doi.org/10.59350/gf1dw-n1v47","uuid":"a41163e0-9c9a-41e0-a141-f772663f2f32","url":"https://iphylo.blogspot.com/2023/03/dugald-stuart-page-1936-2022.html","title":"Dugald
+        as the ill-fated PLoS...","published_at":1637700780,"updated_at":1637701172,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["geocoding","NoCode","RSS"],"language":"en","reference":[{"doi":"https://doi.org/10.1093/bioinformatics/btm109","key":"ref1"},{"doi":"https://doi.org/10.1371/journal.pone.0019491","key":"ref2"},{"key":"ref3","url":"http://arxiv.org/abs/1711.00046"}]},{"id":"20b9d31e-513f-496b-b399-4215306e1588","doi":"https://doi.org/10.59350/en7e9-5s882","url":"https://iphylo.blogspot.com/2022/04/obsidian-markdown-and-taxonomic-trees.html","title":"Obsidian,
+        markdown, and taxonomic trees","summary":"Returning to the subject of personal
+        knowledge graphs Kyle Scheer has an interesting repository of Markdown files
+        that describe academic disciplines at https://github.com/kyletscheer/academic-disciplines
+        (see his blog post for more background). If you add these files to Obsidian
+        you get a nice visualisation of a taxonomy of academic disciplines. The applications
+        of this to biological taxonomy seem obvious, especially as a tool like Obsidian
+        enables all sorts of interesting links to be added...","published_at":1649365620,"updated_at":1649366134,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["markdown","obsidian"],"language":"en","reference":[]},{"id":"d811172e-7798-403c-a83d-3d5317a9657e","doi":"https://doi.org/10.59350/w18j9-v7j10","url":"https://iphylo.blogspot.com/2022/08/papers-citing-data-that-cite-papers.html","title":"Papers
+        citing data that cite papers: CrossRef, DataCite, and the Catalogue of Life","summary":"Quick
+        notes to self following on from a conversation about linking taxonomic names
+        to the literature. Is there a way to turn those links into countable citations
+        (even if just one per database) for Google Scholar?— Wayne Maddison (@WayneMaddison)
+        August 3, 2022 There are different sorts of citation:  Paper cites another
+        paper  Paper cites a dataset  Dataset cites a paper Citation type (1) is largely
+        a solved problem (although there are issues of the ownership and use of this...","published_at":1659526380,"updated_at":1659526393,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["Catalogue of Life","citation","CrossRef","DataCite","DOI"],"language":"en","reference":[]},{"id":"a41163e0-9c9a-41e0-a141-f772663f2f32","doi":"https://doi.org/10.59350/gf1dw-n1v47","url":"https://iphylo.blogspot.com/2023/03/dugald-stuart-page-1936-2022.html","title":"Dugald
         Stuart Page 1936-2022","summary":"My dad died last weekend. Below is a notice
         in today''s New Zealand Herald. I''m in New Zealand for his funeral. Don''t
-        really have the words for this right now.","date_published":"2023-03-14T03:00:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<div class=\"separator\" style=\"clear:
-        both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZweukxntl7R5jnk3knVFVrqZ5RxC7mPZBV4gKeDIglbFzs2O442nbxqs8t8jV2tLqCU24K6gS32jW-Pe8q3O_5JR1Ms3qW1aQAZ877cKkFfcUydqUba9HsgNlX-zS9Ne92eLxRGS8F-lStTecJw2oalp3u58Yoc0oM7CUin5LKPeFIJ7Rzg/s3454/_DSC5106.jpg\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"2582\" data-original-width=\"3454\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZweukxntl7R5jnk3knVFVrqZ5RxC7mPZBV4gKeDIglbFzs2O442nbxqs8t8jV2tLqCU24K6gS32jW-Pe8q3O_5JR1Ms3qW1aQAZ877cKkFfcUydqUba9HsgNlX-zS9Ne92eLxRGS8F-lStTecJw2oalp3u58Yoc0oM7CUin5LKPeFIJ7Rzg/s400/_DSC5106.jpg\"/></a></div>\n\nMy
-        dad died last weekend. Below is a notice in today''s New Zealand Herald. I''m
-        in New Zealand for his funeral. Don''t really have the words for this right
-        now.\n\n<div class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiRUTOFF1VWHCl8dg3FQuaWy5LM7aX8IivdRpTtzgrdQTEymsA5bLTZE3cSQf1WQIP3XrC46JsLScP8BxTK9C5a-B1i51yg8WGSJD0heJVaoDLnerv0lD1o3qloDjqEuuyfX4wagHB5YYBmjWnGeVQvyYVngvDDf9eM6pmMtZ7x94Y4jSVrug/s3640/IMG_2870.jpeg\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" height=\"320\" data-original-height=\"3640\" data-original-width=\"1391\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiRUTOFF1VWHCl8dg3FQuaWy5LM7aX8IivdRpTtzgrdQTEymsA5bLTZE3cSQf1WQIP3XrC46JsLScP8BxTK9C5a-B1i51yg8WGSJD0heJVaoDLnerv0lD1o3qloDjqEuuyfX4wagHB5YYBmjWnGeVQvyYVngvDDf9eM6pmMtZ7x94Y4jSVrug/s320/IMG_2870.jpeg\"/></a></div>","tags":[],"language":"en","references":null},{"id":"https://doi.org/10.59350/c79vq-7rr11","uuid":"3cb94422-5506-4e24-a41c-a250bb521ee0","url":"https://iphylo.blogspot.com/2021/12/graphql-for-wikidata-wikicite.html","title":"GraphQL
-        for WikiData (WikiCite)","summary":"I''ve released a very crude GraphQL endpoint
-        for WikiData. More precisely, the endpoint is for a subset of the entities
-        that are of interest to WikiCite, such as scholarly articles, people, and
-        journals. There is a crude demo at https://wikicite-graphql.herokuapp.com.
-        The endpoint itself is at https://wikicite-graphql.herokuapp.com/gql.php.
-        There are various ways to interact with the endpoint, personally I like the
-        Altair GraphQL Client by Samuel Imolorhe. As I''ve mentioned earlier it''s
-        taken...","date_published":"2021-12-20T13:16:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<div class=\"separator\" style=\"clear:
-        both;\"><a href=\"https://blogger.googleusercontent.com/img/a/AVvXsEh7WW8TlfN2u3xe_E-sH5IK6AWYnAoWaKrP2b32UawUeqMpPlq6ZFk5BtJVZsMmCNh5j3QRsTj5H0Ee55RRGntnc9yjj_mNB8KHmH2dzocCgyLS2VFOxsBji6u4Ey6qxlDAnT-zrsBpnDcTchbhgt1x0Sf7RkmIMkS1y4-_3KCQian-SeIF-g=s1000\"
-        style=\"display: block; padding: 1em 0; text-align: center; clear: right;
-        float: right;\"><img alt=\"\" border=\"0\" width=\"128\" data-original-height=\"1000\"
-        data-original-width=\"1000\" src=\"https://blogger.googleusercontent.com/img/a/AVvXsEh7WW8TlfN2u3xe_E-sH5IK6AWYnAoWaKrP2b32UawUeqMpPlq6ZFk5BtJVZsMmCNh5j3QRsTj5H0Ee55RRGntnc9yjj_mNB8KHmH2dzocCgyLS2VFOxsBji6u4Ey6qxlDAnT-zrsBpnDcTchbhgt1x0Sf7RkmIMkS1y4-_3KCQian-SeIF-g=s200\"/></a></div><p>I''ve
-        released a very crude GraphQL endpoint for WikiData. More precisely, the endpoint
-        is for a subset of the entities that are of interest to WikiCite, such as
-        scholarly articles, people, and journals. There is a crude demo at <a href=\"https://wikicite-graphql.herokuapp.com\">https://wikicite-graphql.herokuapp.com</a>.
-        The endpoint itself is at <a href=\"https://wikicite-graphql.herokuapp.com/gql.php\">https://wikicite-graphql.herokuapp.com/gql.php</a>.
-        There are various ways to interact with the endpoint, personally I like the
-        <a href=\"https://altair.sirmuel.design\">Altair GraphQL Client</a> by <a
-        href=\"https://github.com/imolorhe\">Samuel Imolorhe</a>.</p>\n\n<p>As I''ve
-        <a href=\"https://iphylo.blogspot.com/2021/04/it-been-while.html\">mentioned
-        earlier</a> it''s taken me a while to see the point of GraphQL. But it is
-        clear it is gaining traction in the biodiversity world (see for example the
-        <a href=\"https://dev.gbif.org/hosted-portals.html\">GBIF Hosted Portals</a>)
-        so it''s worth exploring. My take on GraphQL is that it is a way to create
-        a self-describing API that someone developing a web site can use without them
-        having to bury themselves in the gory details of how data is internally modelled.
-        For example, WikiData''s query interface uses SPARQL, a powerful language
-        that has a steep learning curve (in part because of the administrative overhead
-        brought by RDF namespaces, etc.). In my previous SPARQL-based projects such
-        as <a href=\"https://ozymandias-demo.herokuapp.com\">Ozymandias</a> and <a
-        href=\"http://alec-demo.herokuapp.com\">ALEC</a> I have either returned SPARQL
-        results directly (Ozymandias) or formatted SPARQL results as <a href=\"https://schema.org/DataFeed\">schema.org
-        DataFeeds</a> (equivalent to RSS feeds) (ALEC). Both approaches work, but
-        they are project-specific and if anyone else tried to build based on these
-        projects they might struggle for figure out what was going on. I certainly
-        struggle, and I wrote them!</p>\n\n<p>So it seems worthwhile to explore this
-        approach a little further and see if I can develop a GraphQL interface that
-        can be used to build the sort of rich apps that I want to see. The demo I''ve
-        created uses SPARQL under the hood to provide responses to the GraphQL queries.
-        So in this sense it''s not replacing SPARQL, it''s simply providing a (hopefully)
-        simpler overlay on top of SPARQL so that we can retrieve the data we want
-        without having to learn the intricacies of SPARQL, nor how Wikidata models
-        publications and people.</p>","tags":["GraphQL","SPARQL","WikiCite","Wikidata"],"language":"en","references":null},{"id":"https://doi.org/10.59350/ymc6x-rx659","uuid":"0807f515-f31d-4e2c-9e6f-78c3a9668b9d","url":"https://iphylo.blogspot.com/2022/09/dna-barcoding-as-intergenerational.html","title":"DNA
-        barcoding as intergenerational transfer of taxonomic knowledge","summary":"I
-        tweeted about this but want to bookmark it for later as well. The paper “A
-        molecular-based identification resource for the arthropods of Finland” doi:10.1111/1755-0998.13510
-        contains the following: …the annotated barcode records assembled by FinBOL
-        participants represent a tremendous intergenerational transfer of taxonomic
-        knowledge … the time contributed by current taxonomists in identifying and
-        contributing voucher specimens represents a great gift to future generations
-        who will benefit...","date_published":"2022-09-14T10:12:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>I <a href=\"https://twitter.com/rdmpage/status/1569738844416638981?s=21&amp;t=9OVXuoUEwZtQt-Ldzlutfw\">tweeted
-        about this</a> but want to bookmark it for later as well. The paper “A molecular-based
-        identification resource for the arthropods of Finland” <a href=\"https://doi.org/10.1111/1755-0998.13510\">doi:10.1111/1755-0998.13510</a>
-        contains the following:</p>\n<blockquote>\n<p>…the annotated barcode records
-        assembled by FinBOL participants represent a tremendous <mark>intergenerational
-        transfer of taxonomic knowledge</mark> … the time contributed by current taxonomists
-        in identifying and contributing voucher specimens represents a great gift
-        to future generations who will benefit from their expertise when they are
-        no longer able to process new material.</p>\n</blockquote>\n<p>I think this
-        is a very clever way to characterise the project. In an age of machine learning
-        this may be commonest way to share knowledge , namely as expert-labelled training
-        data used to build tools for others. Of course, this means the expertise itself
-        may be lost, which has implications for updating the models if the data isn’t
-        complete. But it speaks to Charles Godfrey’s theme of  <a href=\"https://biostor.org/reference/250587\">“Taxonomy
-        as information science”</a>.</p>\n<p>Note that the knowledge is also transformed
-        in the sense that the underlying expertise of interpreting morphology, ecology,
-        behaviour, genomics, and the past literature is not what is being passed on.
-        Instead it is probabilities that a DNA sequence belongs to a particular taxon.</p>\n<p>This
-        feels is different to, say iNaturalist, where there is a machine learning
-        model to identify images. In that case, the model is built on something the
-        community itself has created, and continues to create. Yes, the underlying
-        idea is that same: “experts” have labelled the data, a model is trained, the
-        model is used. But the benefits of the <a href=\"https://www.inaturalist.org\">iNaturalist</a>
-        model are immediately applicable to the people whose data built the model.
-        In the case of barcoding, because the technology itself is still not in the
-        hands of many (relative to, say, digital imaging), the benefits are perhaps
-        less tangible. Obviously researchers working with environmental DNA will find
-        it very useful, but broader impact may await the arrival of citizen science
-        DNA barcoding.</p>\n<p>The other consideration is whether the barcoding helps
-        taxonomists. Is it to be used to help prioritise future work (“we are getting
-        lots of unknown sequences in these taxa, lets do some taxonomy there”), or
-        is it simply capturing the knowledge of a generation that won’t be replaced:</p>\n<blockquote>\n<p>The
-        need to capture such knowledge is essential because there are, for example,
-        no young Finnish taxonomists who can critically identify species in many key
-        groups of ar- thropods (e.g., aphids, chewing lice, chalcid wasps, gall midges,
-        most mite lineages).</p>\n</blockquote>\n<p>The cycle of collect data, test
-        and refine model, collect more data, rinse and repeat that happens with iNaturalist
-        creates a feedback loop. It’s not clear that a similar cycle exists for DNA
-        barcoding.</p>\n<blockquote>\n<p>Written with <a href=\"https://stackedit.io/\">StackEdit</a>.</p>\n</blockquote>","tags":[],"language":"en","references":null},{"id":"https://doi.org/10.59350/enxas-arj18","uuid":"ab5a6e04-d55e-4901-8269-9eea65ce7178","url":"https://iphylo.blogspot.com/2022/08/can-we-use-citation-graph-to-measure.html","title":"Can
+        really have the words for this right now.","published_at":1678762800,"updated_at":1679469956,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":[],"language":"en","reference":[]},{"id":"8bc3fea6-cb86-4344-8dad-f312fbf58041","doi":"https://doi.org/10.59350/t6fb9-4fn44","url":"https://iphylo.blogspot.com/2021/12/the-business-of-extracting-knowledge.html","title":"The
+        Business of Extracting Knowledge from Academic Publications","summary":"Markus
+        Strasser (@mkstra write a fascinating article entitled \"The Business of Extracting
+        Knowledge from Academic Publications\". I spent months working on domain-specific
+        search engines and knowledge discovery apps for biomedicine and eventually
+        figured that synthesizing \"insights\" or building knowledge graphs by machine-reading
+        the academic literature (papers) is *barely useful* :https://t.co/eciOg30Odc—
+        Markus Strasser (@mkstra) December 7, 2021 His TL;DR: TL;DR: I...","published_at":1639180860,"updated_at":1639180881,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["ai","business model","text mining"],"language":"en","reference":[]},{"id":"96fa91d5-459c-482f-aa38-dda6e0a30e20","doi":"https://doi.org/10.59350/7esgr-61v1","url":"https://iphylo.blogspot.com/2022/01/large-graph-viewer-experiments.html","title":"Large
+        graph viewer experiments","summary":"I keep returning to the problem of viewing
+        large graphs and trees, which means my hard drive has accumulated lots of
+        failed prototypes. Inspired by some recent discussions on comparing taxonomic
+        classifications I decided to package one of these (wildly incomplete) prototypes
+        up so that I can document the idea and put the code somewhere safe. Very cool,
+        thanks for sharing this-- the tree diff is similar to what J Rees has been
+        cooking up lately with his ''cl diff'' tool. I''ll tag...","published_at":1641122700,"updated_at":1641122959,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["Google Maps","graph","Mammal Species of the
+        World","mammals","taxonomy"],"language":"en","reference":[]},{"id":"ab5a6e04-d55e-4901-8269-9eea65ce7178","doi":"https://doi.org/10.59350/enxas-arj18","url":"https://iphylo.blogspot.com/2022/08/can-we-use-citation-graph-to-measure.html","title":"Can
         we use the citation graph to measure the quality of a taxonomic database?","summary":"More
         arm-waving notes on taxonomic databases. I''ve started to add data to ChecklistBank
         and this has got me thinking about the issue of data quality. When you add
@@ -1417,375 +243,34 @@ http_interactions:
         on the Catalogue of Life Checklist Confidence system of one - five stars:
         ★ - ★★★★★. I''m scepetical about the notion of confidence or \"trust\" when
         it is reduced to a star system (see also Can you trust EOL?). I could literally
-        pick any number of stars, there''s...","date_published":"2022-08-24T14:33:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>More arm-waving notes on
-        taxonomic databases. I''ve started to add data to <a href=\"https://www.checklistbank.org\">ChecklistBank</a>
-        and this has got me thinking about the issue of data quality. When you add
-        data to ChecklistBank you are asked to give a measure of confidence based
-        on the <a href=\"https://www.catalogueoflife.org/about/glossary.html#checklist-confidence\">Catalogue
-        of Life Checklist Confidence</a> system of one - five stars: ★ - ★★★★★. I''m
-        scepetical about the notion of confidence or \"trust\" when it is reduced
-        to a star system (see also <a href=\"https://iphylo.blogspot.com/2012/06/can-you-trust-eol.html\">Can
-        you trust EOL?</a>). I could literally pick any number of stars, there''s
-        no way to measure what number of stars is appropriate. This feeds into my
-        biggest reservation about the <a href=\"https://www.catalogueoflife.org\">Catalogue
-        of Life</a>, it''s almost entirely authority based, not evidence based. That
-        is, rather than give us evidence for why a particular taxon is valid, we are
-        (mostly) just given a list of taxa are asked to accept those as gospel, based
-        on assertions by one or more authorities. I''m not necessarly doubting the
-        knowledge of those making these lists, it''s just that I think we need to
-        do better than \"these are the accepted taxa because I say so\" implict in
-        the Catalogue of Life.\n</p>\n\n<p>So, is there any way we could objectively
-        measure the quality of a particular taxonomic checklist? Since I have a long
-        standing interest in link the primary taxonomic litertaure to names in databases
-        (since that''s where the evidence is), I keep wondering whether measures based
-        on that literture could be developed. \n</p>\n<p>\nI recently revisited the
-        fascinating (and quite old) literature on rates of synonymy:\n</p>\n<blockquote>\nGaston
-        Kevin J.  and Mound Laurence A.  1993 Taxonomy, hypothesis testing and the
-        biodiversity crisisProc. R. Soc. Lond. B.251139–142\n<a href=\"http://doi.org/10.1098/rspb.1993.0020\">http://doi.org/10.1098/rspb.1993.0020</a>\n</blockquote>\n  \n<blockquote>\n  Andrew
-        R. Solow, Laurence A. Mound, Kevin J. Gaston, Estimating the Rate of Synonymy,
-        Systematic Biology, Volume 44, Issue 1, March 1995, Pages 93–96, <a href=\"https://doi.org/10.1093/sysbio/44.1.93\">https://doi.org/10.1093/sysbio/44.1.93</a>\n</blockquote>\n\n</p>\n\n<p>\nA
-        key point these papers make is that the observed rate of synonymy is quite
-        high (that is, many \"new species\" end up being merged with already known
-        species), and that because it can take time to discover that a species is
-        a synonym the actual rate may be even higher. In other words, in diagrams
-        like the one reproduced below, the reason the proportion of synonyms declines
-        the nearer we get to the present day (this paper came out in 1995) is not
-        because are are creating fewer synonyms but because we''ve not yet had time
-        to do the work to uncover the remaining synonyms.\n</p>\n  \n<div class=\"separator\"
-        style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhgwvBcDUD_IJZyAa0gaqXB--ogJeVooV19I635N_w2OuztDFsy-ZPXEFuW5S1NUxxUEHmN8pbdO9MPljIi5v0A2355kYotL1fKqdewP9kmWu9TfwtIJ3jD04SQjeF3SWK-yMVAx-rNc6TO43GIwmftPk6IghOrcmur6SoHe06ws7fEFAvxA/s621/Screenshot%202022-08-24%20at%2014.59.47.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"404\" data-original-width=\"621\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhgwvBcDUD_IJZyAa0gaqXB--ogJeVooV19I635N_w2OuztDFsy-ZPXEFuW5S1NUxxUEHmN8pbdO9MPljIi5v0A2355kYotL1fKqdewP9kmWu9TfwtIJ3jD04SQjeF3SWK-yMVAx-rNc6TO43GIwmftPk6IghOrcmur6SoHe06ws7fEFAvxA/s400/Screenshot%202022-08-24%20at%2014.59.47.png\"/></a></div>\n\n<p>Put
-        another way, these papers are arguing that real work of taxonomy is revision,
-        not species discovery, especially since it''s not uncommon for > 50% of species
-        in a taxon to end up being synonymised. Indeed, if a taxoomic group has few
-        synonyms then these authors would argue that''s a sign of neglect. More revisionary
-        work would likely uncover additional synonyms. So, what we need is a way to
-        measure the amount of research on a taxonomic group. It occurs to me that
-        we could use the citation graph as a way to tackle this. Lets imagine we have
-        a set of taxa (say a family) and we have all the papers that described new
-        species or undertook revisions (or both). The extensiveness of that work could
-        be measured by the citation graph. For example, build the citation graph for
-        those papers. How many original species decsriptions are not cited? Those
-        species have been potentially neglected. How many large-scale revisions have
-        there been (as measured by the numbers of taxonomic papers those revisions
-        cite)? There are some interesting approaches to quantifying this, such as
-        using <a href=\"https://en.wikipedia.org/wiki/HITS_algorithm\">hubs and authorities</a>.</p>\n  \n  \n<p>I''m
-        aware that taxonomists have not had the happiest relationship with citations:\n  \n<blockquote>\nPinto
-        ÂP, Mejdalani G, Mounce R, Silveira LF, Marinoni L, Rafael JA. Are publications
-        on zoological taxonomy under attack? R Soc Open Sci. 2021 Feb 10;8(2):201617.
-        <a href=\"https://doi.org/10.1098/rsos.201617\">doi: 10.1098/rsos.201617</a>.
-        PMID: 33972859; PMCID: PMC8074659.\n</blockquote>\n\nStill, I think there
-        is an intriguing possibility here. For this approach to work, we need to have
-        linked taxonomic names to publications, and have citation data for those publications.
-        This is happening on various platforms. Wikidata, for example, is becoming
-        a repository of the taxonomic literature, some of it with citation links.\n\n<blockquote>\nPage
-        RDM. 2022. Wikidata and the bibliography of life. PeerJ 10:e13712 <a href=\"https://doi.org/10.7717/peerj.13712\">https://doi.org/10.7717/peerj.13712</a>\n</blockquote>\n\nTime
-        for some experiments.\n</p>","tags":["Bibliography of Life","citation","synonymy","taxonomic
-        databases"],"language":"en","references":null},{"id":"https://doi.org/10.59350/cbzgz-p8428","uuid":"a93134aa-8b33-4dc7-8cd4-76cdf64732f4","url":"https://iphylo.blogspot.com/2023/04/library-interfaces-knowledge-graphs-and.html","title":"Library
-        interfaces, knowledge graphs, and Miller columns","summary":"Some quick notes
-        on interface ideas for digital libraries and/or knowledge graphs. Recently
-        there’s been something of an explosion in bibliographic tools to explore the
-        literature. Examples include: Elicit which uses AI to search for and summarise
-        papers _scite which uses AI to do sentiment analysis on citations (does paper
-        A cite paper B favourably or not?) ResearchRabbit which uses lists, networks,
-        and timelines to discover related research Scispace which navigates connections
-        between...","date_published":"2023-04-25T13:01:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>Some quick notes on interface
-        ideas for digital libraries and/or knowledge graphs.</p>\n<p>Recently there’s
-        been something of an explosion in bibliographic tools to explore the literature.
-        Examples include:</p>\n<ul>\n<li><a href=\"https://elicit.org\">Elicit</a>
-        which uses AI to search for and summarise papers</li>\n<li><a href=\"https://scite.ai\">_scite</a>
-        which uses AI to do sentiment analysis on citations (does paper A cite paper
-        B favourably or not?)</li>\n<li><a href=\"https://www.researchrabbit.ai\">ResearchRabbit</a>
-        which uses lists, networks, and timelines to discover related research</li>\n<li><a
-        href=\"https://typeset.io\">Scispace</a> which navigates connections between
-        papers, authors, topics, etc., and provides AI summaries.</li>\n</ul>\n<p>As
-        an aside, I think these (and similar tools) are a great example of how bibliographic
-        data such as abstracts, the citation graph and - to a lesser extent - full
-        text - have become commodities. That is, what was once proprietary information
-        is now free to anyone, which in turns means a whole ecosystem of new tools
-        can emerge. If I was clever I’d be building a <a href=\"https://en.wikipedia.org/wiki/Wardley_map\">Wardley
-        map</a> to explore this. Note that a decade or so ago reference managers like
-        <a href=\"https://www.zotero.org\">Zotero</a> were made possible by publishers
-        exposing basic bibliographic data on their articles. As we move to <a href=\"https://i4oc.org\">open
-        citations</a> we are seeing the next generation of tools.</p>\n<p>Back to
-        my main topic. As usual, rather than focus on what these tools do I’m more
-        interested in how they <strong>look</strong>. I have history here, when the
-        iPad came out I was intrigued by the possibilities it offered for displaying
-        academic articles, as discussed <a href=\"https://iphylo.blogspot.com/2010/08/viewing-scientific-articles-on-ipad.html\">here</a>,
-        <a href=\"https://iphylo.blogspot.com/2010/09/viewing-scientific-articles-on-ipad.html\">here</a>,
-        <a href=\"https://iphylo.blogspot.com/2010/08/viewing-scientific-articles-on-ipad_24.html\">here</a>,
-        <a href=\"https://iphylo.blogspot.com/2010/08/viewing-scientific-articles-on-ipad_3052.html\">here</a>,
-        and <a href=\"https://iphylo.blogspot.com/2010/08/viewing-scientific-articles-on-ipad_31.html\">here</a>.
-        ResearchRabbit looks like this:</p>\n<div style=\"padding:86.91% 0 0 0;position:relative;\"><iframe
-        src=\"https://player.vimeo.com/video/820871442?h=23b05b0dae&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479\"
-        frameborder=\"0\" allow=\"autoplay; fullscreen; picture-in-picture\" allowfullscreen
-        style=\"position:absolute;top:0;left:0;width:100%;height:100%;\" title=\"ResearchRabbit\"></iframe></div><script
-        src=\"https://player.vimeo.com/api/player.js\"></script>\n<p>Scispace’s <a
-        href=\"https://typeset.io/explore/journals/parassitologia-1ieodjwe\">“trace”
-        view</a> looks like this:</p>\n<div style=\"padding:84.55% 0 0 0;position:relative;\"><iframe
-        src=\"https://player.vimeo.com/video/820871348?h=2db7b661ef&amp;badge=0&amp;autopause=0&amp;player_id=0&amp;app_id=58479\"
-        frameborder=\"0\" allow=\"autoplay; fullscreen; picture-in-picture\" allowfullscreen
-        style=\"position:absolute;top:0;left:0;width:100%;height:100%;\" title=\"Scispace
-        screencast\"></iframe></div><script src=\"https://player.vimeo.com/api/player.js\"></script>\n<p>What
-        is interesting about both is that they display content from left to right
-        in vertical columns, rather than the more common horizontal rows. This sort
-        of display is sometimes called <a href=\"https://en.wikipedia.org/wiki/Miller_columns\">Miller
-        columns</a> or a <a href=\"https://web.archive.org/web/20210726134921/http://designinginterfaces.com/firstedition/index.php?page=Cascading_Lists\">cascading
-        list</a>.</p>\n\n<div class=\"separator\" style=\"clear: both;\"><a href=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjBPnV9fRBcvm-BX5PjzfG5Cff9PerCLsTW8d5ZbsL6b41t7ypD7ovmcgfTf3b4b34mbq8NM4sfwOHkgEq32FLYnD497RFQD4HQmYmh5Eveu1zWdDVyKyDtPyE98QoxTaOEnLA5kK0fnl3dOOEgUvtVKlTZ8bt1gj2v_8tDRWl9f50ybyei3A/s1024/GNUstep-liveCD.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"768\" data-original-width=\"1024\"
-        src=\"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjBPnV9fRBcvm-BX5PjzfG5Cff9PerCLsTW8d5ZbsL6b41t7ypD7ovmcgfTf3b4b34mbq8NM4sfwOHkgEq32FLYnD497RFQD4HQmYmh5Eveu1zWdDVyKyDtPyE98QoxTaOEnLA5kK0fnl3dOOEgUvtVKlTZ8bt1gj2v_8tDRWl9f50ybyei3A/s400/GNUstep-liveCD.png\"/></a></div>\n\n<p>By
-        Gürkan Sengün (talk) - Own work, Public Domain, <a href=\"https://commons.wikimedia.org/w/index.php?curid=594715\">https://commons.wikimedia.org/w/index.php?curid=594715</a></p>\n<p>I’ve
-        always found displaying a knowledge graph to be a challenge, as discussed
-        <a href=\"https://iphylo.blogspot.com/2019/07/notes-on-collections-knowledge-graphs.html\">elsewhere
-        on this blog</a> and in my paper on <a href=\"https://peerj.com/articles/6739/#p-29\">Ozymandias</a>.
-        Miller columns enable one to drill down in increasing depth, but it doesn’t
-        need to be a tree, it can be a path within a network. What I like about ResearchRabbit
-        and the original Scispace interface is that they present the current item
-        together with a list of possible connections (e.g., authors, citations) that
-        you can drill down on. Clicking on these will result in a new column being
-        appended to the right, with a view (typically a list) of the next candidates
-        to visit. In graph terms, these are adjacent nodes to the original item.  The
-        clickable badges on each item can be thought of as sets of edges that have
-        the same label (e.g., “authored by”, “cites”, “funded”, “is about”, etc.).
-        Each of these nodes itself becomes a starting point for further exploration.
-        Note that the original starting point isn’t privileged, other than being the
-        starting point. That is, each time we drill down we are seeing the same type
-        of information displayed in the same way. Note also that the navigation can
-        be though of as a <strong>card</strong> for a node, with <strong>buttons</strong>
-        grouping the adjacent nodes. When we click on an individual button, it expands
-        into a <strong>list</strong> in the next column. This can be thought of as
-        a preview for each adjacent node. Clicking on an element in the list generates
-        a new card (we are viewing a single node) and we get another set of buttons
-        corresponding to the adjacent nodes.</p>\n<p>One important behaviour in a
-        Miller column interface is that the current path can be pruned at any point.
-        If we go back (i.e., scroll to the left) and click on another tab on an item,
-        everything downstream of that item (i.e., to the right) gets deleted and replaced
-        by a new set of nodes. This could make retrieving a particular history of
-        browsing a bit tricky, but encourages exploration. Both Scispace and ResearchRabbit  have
-        the ability to add items to a collection, so you can keep track of things
-        you discover.</p>\n<p>Lots of food for thought, I’m assuming that there is
-        some user interface/experience research on Miller columns. One thing to remember
-        is that Miller columns are most often associated with trees, but in this case
-        we are exploring a network. That means that potentially there is no limit
-        to the number of columns being generated as we wander through the graph. It
-        will be interesting to think about what the average depth is likely to be,
-        in other words, how deep down the rabbit hole will be go?</p>\n\n<h3>Update</h3>\n<p>Should
-        add link to David Regev''s explorations of <a href=\"https://medium.com/david-regev-on-ux/flow-browser-b730daf0f717\">Flow
-        Browser</a>.\n\n<blockquote>\n<p>Written with <a href=\"https://stackedit.io/\">StackEdit</a>.</p>\n</blockquote>","tags":["cards","flow","Knowledge
-        Graph","Miller column","RabbitResearch"],"language":"en","references":null},{"id":"https://doi.org/10.59350/t6fb9-4fn44","uuid":"8bc3fea6-cb86-4344-8dad-f312fbf58041","url":"https://iphylo.blogspot.com/2021/12/the-business-of-extracting-knowledge.html","title":"The
-        Business of Extracting Knowledge from Academic Publications","summary":"Markus
-        Strasser (@mkstra write a fascinating article entitled \"The Business of Extracting
-        Knowledge from Academic Publications\". I spent months working on domain-specific
-        search engines and knowledge discovery apps for biomedicine and eventually
-        figured that synthesizing &quot;insights&quot; or building knowledge graphs
-        by machine-reading the academic literature (papers) is *barely useful* :https://t.co/eciOg30Odc&mdash;
-        Markus Strasser (@mkstra) December 7, 2021 His TL;DR: TL;DR: I...","date_published":"2021-12-11T00:01:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>Markus Strasser (<a href=\"https://twitter.com/mkstra\">@mkstra</a>
-        write a fascinating article entitled <a href=\"https://markusstrasser.org/extracting-knowledge-from-literature/\">\"The
-        Business of Extracting Knowledge from Academic Publications\"</a>.</p>\n\n<blockquote
-        class=\"twitter-tweet\"><p lang=\"en\" dir=\"ltr\">I spent months working
-        on domain-specific search engines and knowledge discovery apps for biomedicine
-        and eventually figured that synthesizing &quot;insights&quot; or building
-        knowledge graphs by machine-reading the academic literature (papers) is *barely
-        useful* :<a href=\"https://t.co/eciOg30Odc\">https://t.co/eciOg30Odc</a></p>&mdash;
-        Markus Strasser (@mkstra) <a href=\"https://twitter.com/mkstra/status/1468334482113523716?ref_src=twsrc%5Etfw\">December
-        7, 2021</a></blockquote> <script async src=\"https://platform.twitter.com/widgets.js\"
-        charset=\"utf-8\"></script>\n\n<p>His TL;DR:</p>\n\n<p><blockquote>\nTL;DR:
-        I worked on biomedical literature search, discovery and recommender web applications
-        for many months and concluded that extracting, structuring or synthesizing
-        \"insights\" from academic publications (papers) or building knowledge bases
-        from a domain corpus of literature has negligible value in industry.</p>\n\n<p>Close
-        to nothing of what makes science actually work is published as text on the
-        web.\n</blockquote></p>\n\n<p>After recounting the many problems of knowledge
-        extraction - including a swipe at nanopubs which \"are ... dead in my view
-        (without admitting it)\" - he concludes:</p>\n\n<p><blockquote>\nI’ve been
-        flirting with this entire cluster of ideas including open source web annotation,
-        semantic search and semantic web, public knowledge graphs, nano-publications,
-        knowledge maps, interoperable protocols and structured data, serendipitous
-        discovery apps, knowledge organization, communal sense making and academic
-        literature/publishing toolchains for a few years on and off ... nothing of
-        it will go anywhere.</p>\n\n<p>Don’t take that as a challenge. Take it as
-        a red flag and run. Run towards better problems.\n</blockquote></p>\n\n<p>Well
-        worth a read, and much food for thought.</p>","tags":["ai","business model","text
-        mining"],"language":"en","references":null},{"id":"https://doi.org/10.59350/463yw-pbj26","uuid":"dc829ab3-f0f1-40a4-b16d-a36dc0e34166","url":"https://iphylo.blogspot.com/2022/12/david-remsen.html","title":"David
-        Remsen","summary":"I heard yesterday from Martin Kalfatovic (BHL) that David
-        Remsen has died. Very sad news. It''s starting to feel like iPhylo might end
-        up being a list of obituaries of people working on biodiversity informatics
-        (e.g., Scott Federhen). I spent several happy visits at MBL at Woods Hole
-        talking to Dave at the height of the uBio project, which really kickstarted
-        large scale indexing of taxonomic names, and the use of taxonomic name finding
-        tools to index the literature. His work on uBio with David...","date_published":"2022-12-16T17:54:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<p>I heard yesterday from Martin
-        Kalfatovic (BHL) that David Remsen has died. Very sad news. It''s starting
-        to feel like iPhylo might end up being a list of obituaries of people working
-        on biodiversity informatics (e.g., <a href=\"https://iphylo.blogspot.com/2016/05/scott-federhen-rip.html\">Scott
-        Federhen</a>).</p>\n\n<p>I spent several happy visits at MBL at Woods Hole
-        talking to Dave at the height of the uBio project, which really kickstarted
-        large scale indexing of taxonomic names, and the use of taxonomic name finding
-        tools to index the literature. His work on uBio with David (\"Paddy\") Patterson
-        led to the <a href=\"https://eol.org\">Encyclopedia of Life</a> (EOL).</p>\n\n<p>A
-        number of the things I''m currently working on are things Dave started. For
-        example, I recently uploaded a version of his dataset for Nomenclator Zoologicus[1]
-        to <a href=\"https://www.checklistbank.org/dataset/126539/about\">ChecklistBank</a>
-        where I''m working on augmenting that original dataset by adding links to
-        the taxonomic literature. My <a href=\"https://biorss.herokuapp.com/?feed=Y291bnRyeT1XT1JMRCZwYXRoPSU1QiUyMkJJT1RBJTIyJTVE\">BioRSS
-        project</a> is essentially an attempt to revive uBioRSS[2] (see <a href=\"https://iphylo.blogspot.com/2021/11/revisiting-rss-to-monitor-latests.html\">Revisiting
-        RSS to monitor the latest taxonomic research</a>).</p>\n\n<p>I have fond memories
-        of those visits to Woods Hole. A very sad day indeed.</p>\n\n<p><b>Update:</b>
-        The David Remsen Memorial Fund has been set up on <a href=\"https://www.gofundme.com/f/david-remsen-memorial-fund\">GoFundMe</a>.</p>\n\n<p>1.
-        Remsen, D. P., Norton, C., & Patterson, D. J. (2006). Taxonomic Informatics
-        Tools for the Electronic Nomenclator Zoologicus. The Biological Bulletin,
-        210(1), 18–24. https://doi.org/10.2307/4134533</p>\n\n<p>2. Patrick R. Leary,
-        David P. Remsen, Catherine N. Norton, David J. Patterson, Indra Neil Sarkar,
-        uBioRSS: Tracking taxonomic literature using RSS, Bioinformatics, Volume 23,
-        Issue 11, June 2007, Pages 1434–1436, https://doi.org/10.1093/bioinformatics/btm109</p>","tags":["David
-        Remsen","obituary","uBio"],"language":"en","references":null},{"id":"https://doi.org/10.59350/pmhat-5ky65","uuid":"5891c709-d139-440f-bacb-06244424587a","url":"https://iphylo.blogspot.com/2021/10/problems-with-plazi-parsing-how.html","title":"Problems
-        with Plazi parsing: how reliable are automated methods for extracting specimens
-        from the literature?","summary":"The Plazi project has become one of the major
-        contributors to GBIF with some 36,000 datasets yielding some 500,000 occurrences
-        (see Plazi''s GBIF page for details). These occurrences are extracted from
-        taxonomic publication using automated methods. New data is published almost
-        daily (see latest treatments). The map below shows the geographic distribution
-        of material citations provided to GBIF by Plazi, which gives you a sense of
-        the size of the dataset. By any metric Plazi represents a...","date_published":"2021-10-25T11:10:00Z","date_modified":null,"authors":[{"url":null,"name":"noreply@blogger.com
-        (Roderic Page)"}],"image":null,"content_html":"<div class=\"separator\" style=\"clear:
-        both;\"><a href=\"https://1.bp.blogspot.com/-oiqSkA53FI4/YXaRAUpRgFI/AAAAAAAAgzY/PbPEOh_VlhIE0aaqqhVQPLAOE5pRULwJACLcBGAsYHQ/s240/Rf7UoXTw_400x400.jpg\"
-        style=\"display: block; padding: 1em 0; text-align: center; clear: right;
-        float: right;\"><img alt=\"\" border=\"0\" width=\"128\" data-original-height=\"240\"
-        data-original-width=\"240\" src=\"https://1.bp.blogspot.com/-oiqSkA53FI4/YXaRAUpRgFI/AAAAAAAAgzY/PbPEOh_VlhIE0aaqqhVQPLAOE5pRULwJACLcBGAsYHQ/s200/Rf7UoXTw_400x400.jpg\"/></a></div><p>The
-        <a href=\"http://plazi.org\">Plazi</a> project has become one of the major
-        contributors to GBIF with some 36,000 datasets yielding some 500,000 occurrences
-        (see <a href=\"https://www.gbif.org/publisher/7ce8aef0-9e92-11dc-8738-b8a03c50a862\">Plazi''s
-        GBIF page</a> for details). These occurrences are extracted from taxonomic
-        publication using automated methods. New data is published almost daily (see
-        <a href=\"https://tb.plazi.org/GgServer/static/newToday.html\">latest treatments</a>).
-        The map below shows the geographic distribution of material citations provided
-        to GBIF by Plazi, which gives you a sense of the size of the dataset.</p>\n\n<div
-        class=\"separator\" style=\"clear: both;\"><a href=\"https://1.bp.blogspot.com/-DCJ4HR8eej8/YXaRQnz22bI/AAAAAAAAgz4/AgRcree6jVgjtQL2ch7IXgtb_Xtx7fkngCPcBGAYYCw/s1030/Screenshot%2B2021-10-24%2Bat%2B20.43.23.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"514\" data-original-width=\"1030\"
-        src=\"https://1.bp.blogspot.com/-DCJ4HR8eej8/YXaRQnz22bI/AAAAAAAAgz4/AgRcree6jVgjtQL2ch7IXgtb_Xtx7fkngCPcBGAYYCw/s400/Screenshot%2B2021-10-24%2Bat%2B20.43.23.png\"/></a></div>\n\n<p>By
-        any metric Plazi represents a considerable achievement. But often when I browse
-        individual records on Plazi I find records that seem clearly incorrect. Text
-        mining the literature is a challenging problem, but at the moment Plazi seems
-        something of a \"black box\". PDFs go in, the content is mined, and data comes
-        up to be displayed on the Plazi web site and uploaded to GBIF. Nowhere does
-        there seem to be an evaluation of how accurate this text mining actually is.
-        Anecdotally it seems to work well in some cases, but in others it produces
-        what can only be described as bogus records.</p>\n\n<h2>Finding errors</h2>\n\n<p>A
-        treatment in Plazi is a block of text (and sometimes illustrations) that refers
-        to a single taxon. Often that text will include a description of the taxon,
-        and list one or more specimens that have been examined. These lists of specimens
-        (\"material citations\") are one of the key bits of information that Plaza
-        extracts from a treatment as these citations get fed into GBIF as occurrences.</p>\n\n<p>To
-        help explore treatments I''ve constructed a simple web site that takes the
-        Plazi identifier for a treatment and displays that treatment with the material
-        citations highlighted. For example, for the Plazi treatment <a href=\"https://tb.plazi.org/GgServer/html/03B5A943FFBB6F02FE27EC94FABEEAE7\">03B5A943FFBB6F02FE27EC94FABEEAE7</a>
-        you can view the marked up version at <a href=\"https://plazi-tester.herokuapp.com/?uri=622F7788-F0A4-449D-814A-5B49CD20B228\">https://plazi-tester.herokuapp.com/?uri=622F7788-F0A4-449D-814A-5B49CD20B228</a>.
-        Below is an example of a material citation with its component parts tagged:</p>\n\n<div
-        class=\"separator\" style=\"clear: both;\"><a href=\"https://1.bp.blogspot.com/-NIGuo9BggdA/YXaRQQrv0QI/AAAAAAAAgz4/SZDcA1jZSN47JMRTWDwSMRpHUShrCeOdgCPcBGAYYCw/s693/Screenshot%2B2021-10-24%2Bat%2B20.59.56.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"94\" data-original-width=\"693\"
-        src=\"https://1.bp.blogspot.com/-NIGuo9BggdA/YXaRQQrv0QI/AAAAAAAAgz4/SZDcA1jZSN47JMRTWDwSMRpHUShrCeOdgCPcBGAYYCw/s400/Screenshot%2B2021-10-24%2Bat%2B20.59.56.png\"/></a></div>\n\n<p>This
-        is an example where Plazi has successfully parsed the specimen. But I keep
-        coming across cases where specimens have not been parsed correctly, resulting
-        in issues such as single specimens being split into multiple records (e.g.,  <a
-        href=\"https://plazi-tester.herokuapp.com/?uri=5244B05EFFC8E20F7BC32056C178F496\">https://plazi-tester.herokuapp.com/?uri=5244B05EFFC8E20F7BC32056C178F496</a>),
-        geographical coordinates being misinterpreted (e.g., <a href=\"https://plazi-tester.herokuapp.com/?uri=0D228E6AFFC2FFEFFF4DE8118C4EE6B9\">https://plazi-tester.herokuapp.com/?uri=0D228E6AFFC2FFEFFF4DE8118C4EE6B9</a>),
-        or collector''s initials being confused with codes for natural history collections
-        (e.g., <a href=\"https://plazi-tester.herokuapp.com/?uri=252C87918B362C05FF20F8C5BFCB3D4E\">https://plazi-tester.herokuapp.com/?uri=252C87918B362C05FF20F8C5BFCB3D4E</a>).</p>\n\n<p>Parsing
-        specimens is a hard problem so it''s not unexpected to find errors. But they
-        do seem common enough to be easily found, which raises the question of just
-        what percentage of these  material citations are correct? How much of the
-        data Plazi feeds to GBIF is correct? How would we know?</p>\n\n<h2>Systemic
-        problems</h2>\n\n<p>Some of the errors I''ve found concern the interpretation
-        of the parsed data. For example, it is striking that despite including marine
-        taxa <b>no</b> Plazi record has a value for depth below sea level (see <a
-        href=\"https://www.gbif.org/occurrence/map?depth=0,9999&publishing_org=7ce8aef0-9e92-11dc-8738-b8a03c50a862&advanced=1\">GBIF
-        search on depth range 0-9999 for Plazi</a>). But <a href=\"https://www.gbif.org/occurrence/map?elevation=0,9999&publishing_org=7ce8aef0-9e92-11dc-8738-b8a03c50a862&advanced=1\">many
-        records do have an elevation</a>, including records from marine environments.
-        Any record that has a depth value is interpreted by Plazi as being elevation,
-        so we have aerial crustacea and fish.</p>\n\n<h3>Map of Plazi records with
-        depth 0-9999m</h3>\n<div class=\"separator\" style=\"clear: both;\"><a href=\"https://1.bp.blogspot.com/-GD4pPtPCxVc/YXaRQ9bdn1I/AAAAAAAAgz8/A9YsypSvHfwWKAjDxSdeFVUkou88LGItACPcBGAYYCw/s673/Screenshot%2B2021-10-25%2Bat%2B12.03.51.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"258\" data-original-width=\"673\"
-        src=\"https://1.bp.blogspot.com/-GD4pPtPCxVc/YXaRQ9bdn1I/AAAAAAAAgz8/A9YsypSvHfwWKAjDxSdeFVUkou88LGItACPcBGAYYCw/s320/Screenshot%2B2021-10-25%2Bat%2B12.03.51.png\"/></a></div>\n\n<h3>Map
-        of Plazi records with elevation 0-9999m </h3>\n<div class=\"separator\" style=\"clear:
-        both;\"><a href=\"https://1.bp.blogspot.com/-BReSHtXTOkA/YXaRRKFW7dI/AAAAAAAAg0A/-FcBkMwyswIp0siWGVX3MNMANs7UkZFtwCPcBGAYYCw/s675/Screenshot%2B2021-10-25%2Bat%2B12.04.06.png\"
-        style=\"display: block; padding: 1em 0; text-align: center; \"><img alt=\"\"
-        border=\"0\" width=\"400\" data-original-height=\"256\" data-original-width=\"675\"
-        src=\"https://1.bp.blogspot.com/-BReSHtXTOkA/YXaRRKFW7dI/AAAAAAAAg0A/-FcBkMwyswIp0siWGVX3MNMANs7UkZFtwCPcBGAYYCw/s320/Screenshot%2B2021-10-25%2Bat%2B12.04.06.png\"/></a></div>\n\n<p>Anecdotally
-        I''ve also noticed that Plazi seems to do well on zoological data, especially
-        journals like <i>Zootaxa</i>, but it often struggles with botanical specimens.
-        Botanists tend to cite specimens rather differently to zoologists (botanists
-        emphasise collector numbers rather than specimen codes). Hence data quality
-        in Plazi is likely to taxonomic biased.</p>\n\n<p>Plazi is <a href=\"https://github.com/plazi/community/issues\">using
-        GitHub to track issues with treatments</a> so feedback on erroneous records
-        is possible, but this seems inadequate to the task. There are tens of thousands
-        of data sets, with more being released daily, and hundreds of thousands of
-        occurrences, and relying on GitHub issues devolves the responsibility for
-        error checking onto the data users. I don''t have a measure of how many records
-        in Plazi have problems, but because I suspect it is a significant fraction
-        because for any given day''s output I can typically find errors.</p>\n\n<h2>What
-        to do?</h2>\n\n<p>Faced with a process that generates noisy data there are
-        several of things we could do:</p>\n\n<ol>\n<li>Have tools to detect and flag
-        errors made in generating the data.</li>\n<li>Have the data generator give
-        estimates the confidence of its results.</li>\n<li>Improve the data generator.</li>\n</ol>\n\n<p>I
-        think a comparison with the problem of parsing bibliographic references might
-        be instructive here. There is a long history of people developing tools to
-        parse references (<a href=\"https://iphylo.blogspot.com/2021/05/finding-citations-of-specimens.html\">I''ve
-        even had a go</a>). State-of-the art tools such as <a href=\"https://anystyle.io\">AnyStyle</a>
-        feature machine learning, and are tested against <a href=\"https://github.com/inukshuk/anystyle/blob/master/res/parser/core.xml\">human
-        curated datasets</a> of tagged bibliographic records. This means we can evaluate
-        the performance of a method (how well does it retrieve the same results as
-        human experts?) and also improve the method by expanding the corpus of training
-        data. Some of these tools can provide a measures of how confident they are
-        when classifying a string as, say, a person''s name, which means we could
-        flag potential issues for anyone wanting to use that record.</p>\n\n<p>We
-        don''t have equivalent tools for parsing specimens in the literature, and
-        hence have no easy way to quantify how good existing methods are, nor do we
-        have a public corpus of material citations that we can use as training data.
-        I <a href=\"https://iphylo.blogspot.com/2021/05/finding-citations-of-specimens.html\">blogged
-        about this</a> a few months ago and was considering using Plazi as a source
-        of marked up specimen data to use for training. However based on what I''ve
-        looked at so far Plazi''s data would need to be carefully scrutinised before
-        it could be used as training data.</p>\n\n<p>Going forward, I think it would
-        be desirable to have a set of records that can be used to benchmark specimen
-        parsers, and ideally have the parsers themselves available as web services
-        so that anyone can evaluate them. Even better would be a way to contribute
-        to the training data so that these tools improve over time.</p>\n\n<p>Plazi''s
-        data extraction tools are mostly desktop-based, that is, you need to download
-        software to use their methods. However, there are experimental web services
-        available as well. I''ve created a simple wrapper around the material citation
-        parser, you can try it at <a href=\"https://plazi-tester.herokuapp.com/parser.php\">https://plazi-tester.herokuapp.com/parser.php</a>.
-        It takes a single material citation and returns a version with elements such
-        as specimen code and collector name tagged in different colours.</p>\n\n<h2>Summary</h2>\n\n<p>Text
-        mining the taxonomic literature is clearly a gold mine of data, but at the
-        same time it is potentially fraught as we try and extract structured data
-        from semi-structured text. Plazi has demonstrated that it is possible to extract
-        a lot of data from the literature, but at the same time the quality of that
-        data seems highly variable. Even minor issues in parsing text can have big
-        implications for data quality (e.g., marine organisms apparently living above
-        sea level). Historically in biodiversity informatics we have favoured data
-        quantity over data quality. Quantity has an obvious metric, and has milestones
-        we can celebrate (e.g., <a href=\"GBIF at 1 billion - what''s next?\">one
-        billion specimens</a>). There aren''t really any equivalent metrics for data
-        quality.</p>\n\n<p>Adding new types of data can sometimes initially result
-        in a new set of quality issues (e.g., <a href=\"https://iphylo.blogspot.com/2019/12/gbif-metagenomics-and-metacrap.html\">GBIF
-        metagenomics and metacrap</a>) that take time to resolve. In the case of Plazi,
-        I think it would be worthwhile to quantify just how many records have errors,
-        and develop benchmarks that we can use to test methods for extracting specimen
-        data from text. If we don''t do this then there will remain uncertainty as
-        to how much trust we can place in data mined from the taxonomic literature.</p>\n\n<h2>Update</h2>\n\nPlazi
-        has responded, see <a href=\"http://plazi.org/posts/2021/10/liberation-first-step-toward-quality/\">Liberating
-        material citations as a first step to more better data</a>. My reading of
-        their repsonse is that it essentially just reiterates Plazi''s approach and
-        doesn''t tackle the underlying issue: their method for extracting material
-        citations is error prone, and many of those errors end up in GBIF.","tags":["data
-        quality","parsing","Plazi","specimen","text mining"],"language":"en","references":null}]}'
-  recorded_at: Thu, 15 Jun 2023 20:47:10 GMT
-recorded_with: VCR 6.1.0
+        pick any number of stars, there''s...","published_at":1661351580,"updated_at":1661351908,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":["Bibliography of Life","citation","synonymy","taxonomic
+        databases"],"language":"en","reference":[]},{"id":"0807f515-f31d-4e2c-9e6f-78c3a9668b9d","doi":"https://doi.org/10.59350/ymc6x-rx659","url":"https://iphylo.blogspot.com/2022/09/dna-barcoding-as-intergenerational.html","title":"DNA
+        barcoding as intergenerational transfer of taxonomic knowledge","summary":"I
+        tweeted about this but want to bookmark it for later as well. The paper “A
+        molecular-based identification resource for the arthropods of Finland” doi:10.1111/1755-0998.13510
+        contains the following: …the annotated barcode records assembled by FinBOL
+        participants represent a tremendous intergenerational transfer of taxonomic
+        knowledge … the time contributed by current taxonomists in identifying and
+        contributing voucher specimens represents a great gift to future generations
+        who will benefit...","published_at":1663150320,"updated_at":1664459850,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":[],"language":"en","reference":[]},{"id":"8aea47e4-f227-45f4-b37b-0454a8a7a3ff","doi":"https://doi.org/10.59350/m48f7-c2128","url":"https://iphylo.blogspot.com/2023/04/chatgpt-semantic-search-and-knowledge.html","title":"ChatGPT,
+        semantic search, and knowledge graphs","summary":"One thing about ChatGPT
+        is it has opened my eyes to some concepts I was dimly aware of but am only
+        now beginning to fully appreciate. ChatGPT enables you ask it questions, but
+        the answers depend on what ChatGPT “knows”. As several people have noted,
+        what would be even better is to be able to run ChatGPT on your own content.
+        Indeed,  ChatGPT itself now supports this using plugins. Paul Graham GPT However,
+        it’s still useful to see how to add ChatGPT functionality to your own content
+        from...","published_at":1680535800,"updated_at":1680535924,"indexed_at":1689006804,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":[],"language":"en","reference":[]},{"id":"9d19993f-a228-4883-8933-be5b5459530d","doi":"https://doi.org/10.59350/r3g44-d5s15","url":"https://iphylo.blogspot.com/2023/06/a-taxonomic-search-engine.html","title":"A
+        taxonomic search engine","summary":"Tony Rees commented on my recent post
+        Ten years and a million links. I’ve responded to some of his comments, but
+        I think the bigger question deserves more space, hence this blog post. Tony’s
+        comment Hi Rod, I like what you’re doing. Still struggling (a little) to find
+        the exact point where it answers the questions that are my “entry points”
+        so to speak, which (paraphrasing a post of yours from some years back) start
+        with: Is this a name that “we” (the human race I suppose) recognise as...","published_at":1687016280,"updated_at":1687016300,"indexed_at":1688982864,"authors":[{"url":"https://orcid.org/0000-0002-7101-9767","name":"Roderic
+        Page"}],"image":null,"tags":[],"language":"en","reference":[]}]}'
+  recorded_at: Mon, 10 Jul 2023 20:37:16 GMT
+recorded_with: VCR 6.2.0