Sven Lieber

<p>Hello everyone,</p><p>welcome to today’s Halloween edition about <em>data anti-patterns</em> that hopefully will scare you so much you don’t do them :-) Things you better avoid when aiming for FAIR data.</p><p>Anti patterns? In short they are the <strong>opposite of best practices</strong>. Common or obvious solutions that are not only <em>ineffective </em>but also <em>risky</em>. Similar to biases, it is good to know about them so you can try avoiding them. I mainly know the term from software engineering, but apparently it is at least also known for project management and business processes (<a href="https://www.wikidata.org/wiki/Q76438">Q76438</a>, <a href="https://en.wikipedia.org/wiki/Anti-pattern">Wikipedia</a>). </p><p>In the following I will list some anti patterns I have seen “in the wild” that directly relate to the FAIR principles, their evil twins if you like 🧛 </p><div class="captioned-image-container"><figure><a class="image-link is-viewable-img image2" target="_blank" href="https://substackcdn.com/image/fetch/f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg" data-component-name="Image2ToDOM"><div class="image2-inset"><picture><source type="image/webp" srcset="https://substackcdn.com/image/fetch/w_424,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg 424w, https://substackcdn.com/image/fetch/w_848,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg 848w, https://substackcdn.com/image/fetch/w_1272,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg 1272w, https://substackcdn.com/image/fetch/w_1456,c_limit,f_webp,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg 1456w" sizes="100vw"><img src="https://substackcdn.com/image/fetch/w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg" width="1280" height="960" data-attrs="{&quot;src&quot;:&quot;https://substack-post-media.s3.amazonaws.com/public/images/76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg&quot;,&quot;srcNoWatermark&quot;:null,&quot;fullscreen&quot;:null,&quot;imageSize&quot;:null,&quot;height&quot;:960,&quot;width&quot;:1280,&quot;resizeWidth&quot;:null,&quot;bytes&quot;:null,&quot;alt&quot;:null,&quot;title&quot;:null,&quot;type&quot;:null,&quot;href&quot;:null,&quot;belowTheFold&quot;:false,&quot;topImage&quot;:true,&quot;internalRedirect&quot;:null}" class="sizing-normal" alt="" srcset="https://substackcdn.com/image/fetch/w_424,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg 424w, https://substackcdn.com/image/fetch/w_848,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg 848w, https://substackcdn.com/image/fetch/w_1272,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg 1272w, https://substackcdn.com/image/fetch/w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F76805904-80e4-4327-a1d9-207dc9916382_1280x960.jpeg 1456w" sizes="100vw" fetchpriority="high"></picture><div class="image-link-expand"><svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="#FFFFFF" stroke-width="2" stroke-linecap="round" stroke-linejoin="round" class="lucide lucide-maximize2"><polyline points="15 3 21 3 21 9"></polyline><polyline points="9 21 3 21 3 15"></polyline><line x1="21" x2="14" y1="3" y2="10"></line><line x1="3" x2="10" y1="21" y2="14"></line></svg></div></div></a><figcaption class="image-caption">daryl_mitchell from Saskatoon, Saskatchewan, Canada, CC BY-SA 2.0, via Wikimedia Commons</figcaption></figure></div><div><hr></div><h2>Findability: the needle in the haystack</h2><p>Findability is probably <em>the </em>most important principle to get started: if you don’t know that something exists or you know it but you don’t know where it is, then you simply cannot use it.</p><p>Providing unique and <strong>persistent identifiers</strong> for things is the common solution to deal with findability. As easy as it sounds, there are many possible pitfalls, some obvious and some more tricky. </p><ul><li><p>😱 reusing identifiers </p><p>➡️ Recycling is good, but reusing identifiers is bad: identifiers should be <strong>unique</strong>!</p></li><li><p>😱 implementation details as part of the identifier </p><p>➡️ If you change your software or provider the identifier will change, hence “identifiers” such as <code>http://my-url.com/items?query=abc</code> are bad.</p></li><li><p>😱 thinking that persistent identifiers are only a technical problem for the ICT department </p><p>➡️ Providing and maintaining the technical infrastructure is important, but knowing the data, use cases, stakeholders and community best practices is just as important</p></li></ul><p>From a very practical perspective, searching nowadays often happen via Google. Did you ever try to google a persistent identifier? Often you won’t find much. The following paper investigates how FAIR persistent identifiers actually are and which role validity can play (DOI: <a href="https://doi.org/10.3233/DS-190024">10.3233/DS-190024</a>).</p><p>By the way, there are different ways to implement persistent identifiers. You can check out the Persistent Identifier Guide of the Dutch Digital Heritage Network to know which system works best for you. Just answer 25 questions.</p><p class="button-wrapper" data-attrs="{&quot;url&quot;:&quot;https://www.pidwijzer.nl/en/&quot;,&quot;text&quot;:&quot;Read the Persistent Identifier Guide&quot;,&quot;action&quot;:null,&quot;class&quot;:null}" data-component-name="ButtonCreateButton"><a class="button primary" href="https://www.pidwijzer.nl/en/"><span>Read the Persistent Identifier Guide</span></a></p><div><hr></div><h2>Accessibility: what’s in the box?!</h2><p>To stay in the Halloween theme, imagine you’ve <em>found </em>a secret door, but you don’t know how to open it. You would be more than happy getting some <em>information </em>about how to <em>access </em>the room behind it: that would be metadata about accessibility.</p><ul><li><p>😱 not providing any metadata</p><p>➡️ <em>“<s>Pics</s> metadata or it didn’t happen”</em>. Help others to find out more about something (something that possibly is no longer available). I have heard that the phone number of a research projects’ PI can be the most valuable piece of metadata :-) (DOI: <a href="https://doi.org/10.5281/zenodo.8344854">10.5281/zenodo.8344854</a>, <a href="https://www.youtube.com/watch?v=3J-jAFldeac">YouTube</a>)</p></li><li><p>😱 not using an open standard for metadata</p><p>➡️ After all the effort of making data available, please go the extra mile of easy accessible metadata, your users will thank you!</p></li></ul><div><hr></div><h2>Interoperability: it just works</h2><p>FAIR's tongue-twister that even grammar checkers have trouble with. Exchanging information between computer systems without re-inventing the wheel each time. It’s all about standards (again).</p><ul><li><p>😱 not using a standard</p><p>➡️ Standards are important, not just to charge your devices via USB, also for your data! Think of the amazing feeling when you can simply double click on a file and it just opens without problems.</p></li><li><p>😱 using a standard in the wrong way</p><p>➡️ Read the docs to use the standard (vocabulary) you are using to describe your data in the correct way. Imagine you annotate your website wrong and therefore it will rank worse on Google and other search engines.</p></li><li><p>😱 using a proprietary format</p><p>➡️ You have done an amazing job to create some valuable data, don’t make its value and success dependent on an untrustworthy commercial product that may cease to exist or that only a fraction of your users are able to use.</p></li></ul><div><hr></div><h2>Reusability:</h2><p>You found something online, for free … how valuable do you think is it for your use case and to which extend are you allowed to use it? Likewise, if you create something you probably want to be credited for, so you should indicate how someone else can reuse what you created. These questions concern the reusability (of data). There are a few things to avoid.</p><ul><li><p>😱 no license</p><p>➡️ No one likes to be sued! Indicate a license to give security to your users on the one hand, and tell them how you would like them to use it on the other hand. </p></li><li><p>😱 don’t mention any sources or provenance</p><p>➡️ Everything has its origin, knowing it is important to assess its value for reuse. Based on which criteria did you curate the data? Which software did you use? Which data sources?</p></li><li><p>😱 too complicated</p><p>➡️ make it easy for anyone to reuse your data/software. Once again, this can be achieved by following standards. For example, when providing code try to follow common coding and installation guidelines.</p></li></ul><p></p><p>These were just a few anti patterns standing opposite to some of the FAIR principles. Feel free to google to find more specific data anti patterns. Happy Halloween 🎃</p><div><hr></div><p>That’s it for this week of the FAIR Data Digest. If you found the content interesting, please share and subscribe. See you <em>in two weeks</em>!</p><p>Sven</p><div class="subscription-widget-wrap" data-attrs="{&quot;url&quot;:&quot;https://fairdata.substack.com/subscribe?&quot;,&quot;text&quot;:&quot;Subscribe&quot;,&quot;language&quot;:&quot;en&quot;}" data-component-name="SubscribeWidgetToDOM"><div class="subscription-widget show-subscribe"><div class="preamble"><p class="cta-caption">Thanks for reading FAIR Data Digest! Subscribe for free to receive new posts and support my work.</p></div><form class="subscription-widget-subscribe"><input type="email" class="email-input" name="email" placeholder="Type your email…" tabindex="-1"><input type="submit" class="button primary" value="Subscribe"><div class="fake-input-wrapper"><div class="fake-input"></div><div class="fake-button"></div></div></form></div></div>

the Halloween edition on scary data anti-patterns


FAIR Data Digest #20

Henry Rzepa

<div class="kcite-section" kcite-section-id="19603">
<p>The site <a href="https://fairsharing.org/">fairsharing.org</a> is a repository of information about FAIR (Findable, Accessible, Interoperable and Reusable) objects such as research data.<br />
 <img loading="lazy" decoding="async" class="aligncenter size-large wp-image-19605" src="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2018/04/240-1024x478.jpg" alt="" width="450" height="210" srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2018/04/240-1024x478.jpg 1024w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2018/04/240-300x140.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2018/04/240-768x358.jpg 768w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2018/04/240.jpg 2044w" sizes="(max-width: 450px) 100vw, 450px" /></p>
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<p>A project to inject chemical components, rather sparse at the moment at the above site, is being promoted by workshops under the auspices of e.g. <a href="https://iupac.org/event/supporting-fair-exchange-chemical-data-standards-development/">IUPAC and CODATA</a> and the <a href="https://www.go-fair.org">GO-FAIR initiative</a>. One aspect of this activity is to help identify examples of both good (FAIR) and indeed less good (unFAIR) research data as associated with contemporary scientific journal publications.</p>
<p>Here is one example I came across in 2017.<span id="cite_ITEM-19603-0" name="citation"><a href="#ITEM-19603-0">[1]</a></span>. The data associated with this article is certainly copious, 907 pages of it, not including data for 21 crystal structures! The latter is a good example of FAIR, being offered in a standard format (CIF) well-adapted for the type of data contained therein and for which there are numerous programs capable of visualising and inter-operating (<em>i.e.</em> re-using) it. The former is in PDF, not a format originally developed for data and one could argue is closer to the unFAIR end of the spectrum. More so when you consider this one 907-page paginated document contains diverse information including spectra on around 60 molecules. Thus the spectra are all purely visual; they are obviously data but in a form largely designed for human consumption and not re-use by software. The text-based content of this PDF does have numerous pattens, which lends itself to pattern recognition software such as OSCAR, but patterns are easily broken by errors or inexperience and so we cannot be certain what proportion of this can be recovered. The metadata associated with such a collection, if there is any at all, must be general and cannot be easily related to specific molecules in the collection. So I would argue that 907 pages of data as wrapped in PDF is not a good example of FAIR. But it is how almost all of the data currently being reported in chemistry journals is expressed. Indeed many a journal data editor (a relatively new introduction to the editorial teams) exerts a rigorous oversight over the data presented as part of article submissions to ensure it adheres to this monolithic PDF format.</p>
<p>You can also visit this article in Chemistry World (<a href="https://rsc.li/2HG7lTk" rel="nofollow">rsc.li/2HG7lTk</a>) for an alternative view of what could be regarded as rather more FAIR data. The article has citations to the FAIR components, which is not published as part of the article or indeed by the journal itself but is held separately in a research data repository. You will find that at doi: <a href="https://doi.org/10.14469/hpc/3657">10.14469/hpc/3657</a> where examples of computational, crystallographic and spectroscopic data are available.</p>
<p>The workshop I allude to above will be held in July. Can I ask anyone reading this blog who has a favourite FAIR or indeed unFAIR example of data they have come across to share these here. We also need to identify areas simply crying out for FAIRer data to be made available as part of the publishing process beyond the types noted above. I hope to report back on both such feedback and the events at this workshop in due course.</p>
<div class="wp_orcid_field"><a href="https://orcid.org/0000-0002-8635-8390" target="_blank" rel="author">https://orcid.org/0000-0002-8635-8390</a></div><h2>References</h2>
    <ol>
    <li><a name='ITEM-19603-0'></a>
J.M. Lopchuk, K. Fjelbye, Y. Kawamata, L.R. Malins, C. Pan, R. Gianatassio, J. Wang, L. Prieto, J. Bradow, T.A. Brandt, M.R. Collins, J. Elleraas, J. Ewanicki, W. Farrell, O.O. Fadeyi, G.M. Gallego, J.J. Mousseau, R. Oliver, N.W. Sach, J.K. Smith, J.E. Spangler, H. Zhu, J. Zhu, and P.S. Baran, "Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity", <i>Journal of the American Chemical Society</i>, vol. 139, pp. 3209-3226, 2017. <a href="http://dx.doi.org/10.1021/jacs.6b13229">http://dx.doi.org/10.1021/jacs.6b13229</a>


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The site fairsharing.org is a repository of information about FAIR (Findable, Accessible, Interoperable and Reusable) objects such as research data. A project to inject chemical components, rather sparse at the moment at the above site, is being promoted by workshops under the auspices of e.g. IUPAC and CODATA and the GO-FAIR initiative.


Rogue Scholar Posts

FAIR Data Digest #20

Examples please of FAIR (data); good and bad.