commonmeta-ruby 3.3.2 → 3.3.4

data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/get_doi_prefix_for_blog/by_blog_id.yml

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+      - Sun, 18 Jun 2023 15:24:19 GMT
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@@ -50,420 +50,7 @@ http_interactions:
         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","feed_format":"application/atom+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
-        7.00","category":"Natural Sciences","backlog":true,"prefix":"10.59350","items":[{"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":"2022-04-07T21:15:34Z","date_indexed":"1909-06-16T09:41:45+00:00","authors":[{"url":null,"name":"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=AD6v5dxZtweOTJTdg6aqvICq_tKF0la1QZuDAEpwPPCVQKtG5vjB-DzuQv-ApL8JnpyZ1FffYtWo6ymizNQ''
-        class=''b-hbp-video b-uploaded'' frameborder=''0''></iframe></div>","tags":["markdown","obsidian"],"language":"en","references":[]},{"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":"2023-04-03T15:32:04Z","date_indexed":"1909-06-16T09:02:34+00:00","authors":[{"url":null,"name":"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":[]},{"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":"2022-09-01T16:49:51Z","date_indexed":"1909-06-16T09:31:50+00:00","authors":[{"url":null,"name":"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":[]},{"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":"2021-10-28T16:08:18Z","date_indexed":"1970-01-01T00:00:00+00:00","authors":[{"url":null,"name":"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":[]},{"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":"2022-08-22T17:19:08Z","date_indexed":"1909-06-16T08:21:41+00:00","authors":[{"url":null,"name":"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":[]},{"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
+        7.00","category":"Natural Sciences","backlog":true,"prefix":"10.59350","items":[{"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
@@ -993,5 +580,5 @@ http_interactions:
         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":[]}]}'
-  recorded_at: Sun, 18 Jun 2023 05:50:13 GMT
+  recorded_at: Sun, 18 Jun 2023 15:24:19 GMT
 recorded_with: VCR 6.1.0