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-      string: '{"id":"tyfqw20","title":"iPhylo","description":"Rants, raves (and occasionally
-        considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics.  For
-        more ranty and less considered opinions, see my <a href=\"https://twitter.com/rdmpage\">Twitter
-        feed</a>.<br>ISSN 2051-8188. Written content on this site is licensed under
-        a <a href=\"https://creativecommons.org/licenses/by/4.0/\">Creative Commons
-        Attribution 4.0 International license</a>.","language":"en","favicon":null,"feed_url":"https://iphylo.blogspot.com/feeds/posts/default","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
-        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":"2022-09-29T13:57:30Z","date_indexed":"1909-06-16T11:02:21+00:00","authors":[{"url":null,"name":"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":[]},{"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":"2021-10-08T10:26:22Z","date_indexed":"1909-06-16T10:02:25+00:00","authors":[{"url":null,"name":"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":[]},{"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
-        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":"2023-03-22T07:25:56Z","date_indexed":"1909-06-16T10:41:55+00:00","authors":[{"url":null,"name":"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":[]},{"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":"2023-04-27T14:51:08Z","date_indexed":"1909-06-16T11:25:14+00:00","authors":[{"url":null,"name":"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":[]},{"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 \"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 worked on biomedical...","date_published":"2021-12-11T00:01:00Z","date_modified":"2021-12-11T00:01:21Z","date_indexed":"1909-06-16T11:32:09+00:00","authors":[{"url":null,"name":"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":[]},{"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":"2022-12-17T08:12:23Z","date_indexed":"1909-06-16T11:41:39+00:00","authors":[{"url":null,"name":"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":[]},{"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
-        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":"2022-02-03T15:11:29Z","date_indexed":"1909-06-16T10:22:30+00:00","authors":[{"url":null,"name":"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":[]},{"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":"2021-12-20T13:20:05Z","date_indexed":"1909-06-16T10:52:00+00:00","authors":[{"url":null,"name":"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":[]}]}'
-  recorded_at: Sun, 18 Jun 2023 06:01:20 GMT
-recorded_with: VCR 6.1.0