bluuebunny/crossref_metadata_2025 huggingface dataset:
Automatic Water Pumping and Quality Monitoring System
Authors:   Department of Electronics and Communication Engineering, Universal Engineering College,  Vallivattom, Thrissur, Kerala, India., R P Hridya , K R Aromal , C Y Anu Treesa , T J Aljo , Edattukaran Elizabeth S
Published: September 2023

This project presents an innovative solution for automatic water pumping and real-time quality monitoring using the Blynk platform. It's designed to enhance water quality and pumping efficiency, ideal for hydroponics, aquaponics, and irrigation. Key components include an Arduino Uno, ultrasonic sensor for liquid levels, a relay for pump control, and a pH sensor. The system maintains water levels within defined thresholds and monitors pH levels, activating the pump when needed. Keywords: Automatic water pumping; Quality monitoring; Arduino UNO; pH sensor; Blynk platform
Displaying a million DNA barcodes on Google Maps using CouchDB
Authors: Page Roderic
Published: September 2023

Following on from the previous post on putting GBIF data onto Google Maps, I'm now going to put DNA barcodes onto Google Maps. You can see the result at http://iphylo.org/~rpage/bold-map/, which displays around 1.2 million barcodes obtained from the International Barcode of Life Project (iBOL) releases.
Towards BioStor articles marked up using Journal Archiving Tag Set
Authors: Page Roderic
Published: September 2023

A while ago I posted BHL to PDF workflow which was a sketch of a work flow to generate clean, searchable PDFs from Biodiversity Heritage Library (BHL) content: I've made some progress on putting this together, as well as expanded the goal somewhat. In fact, there are several goals:BioStor articles need to be archived somewhere. At the moment they live on my server, and metadata is also served by BHL (as the "parts" you see in a scanned volume).
Easy Things Are Hard
Authors: Winston Donny
Published: September 2023

In general, we’re least aware of what our minds do best. It’s mainly when systems start to fail that we engage the special agencies involved with what we call “consciousness.” Accordingly, we’re more aware of simple processes that don’t work well than of complex ones that work flawlessly. This phenomenon helps to explain the poor performance of many so-called  expert systems  in the 1980s.
Agents and Hierarchies
Authors: Winston Donny
Published: September 2023

Designing any society, be it human or computational, involves decisions like these: Which agents choose which others to do what jobs? Who will decide which jobs are done at all? Who decides what efforts to expend? How will conflicts be settled? Furthermore, roles even in a hierarchy are always relative. To  Builder  ,  Add  is a subordinate, but to  Find  ,  Add  is a boss.
Open, Reproducible, Sustainable
Authors: Winston Donny
Published: September 2023

Irving et al.  1  approach digital research infrastructure through three related but distinct concepts: openness, reproducibility, and sustainability. Openness is about making digital resources generally accessible for reuse, sharing, and adaptation through an open license.
The Research Process and the Bits
Authors: Winston Donny
Published: September 2023

How could solid-seeming computer hardware support such a ghostly thing as research progress? The world of scientific inquiry and the world of bits appear too far apart to interact in any way. A few centuries ago it seemed impossible to explain Life - living things appeared to be so different from anything else. Last century, von Neumann helped show how cell-machines could reproduce.
Mark-up of biodiversity literature
Authors: Page Roderic
Published: September 2023

I gave a remote presentation at a proiBioSphere workshop this morning. The slides are below (to try and make it a bit more engaging than a desk of Powerpoints I played around with Prezi).There is a version on Vimeo that has audio as well.I sketched out the biodiversity "knowledge graph", then talked about how mark-up relates to this, finishing with a few questions.
ITIS and DOIs
Authors: Page Roderic
Published: September 2023

Following on from my earlier grumble about how the catalogue of Life handles literature, I've spent an afternoon mapping publications in the  "itis".publications  table in a copy of ITIS to external GUIDs, such as DOIs, Handles, and SICIs in JSTOR. The mapping is not complete by any means, but gives an idea of how many publications have GUIDs.You can view the mapping here. Many of the publications in ITIS are books, which don't have DOIs.
Common Sense
Authors: Winston Donny
Published: September 2023

We found a way to make a tower builder out of parts. But  Builder  is really far from done. For example, how could  Find  determine which blocks are still available for use? It would have to “understand” the scene in terms of what it is trying to do. We’ll need theories both about what it means to understand and about how a machine could have a goal.
A Delimiters-in-Front Coding Style
Authors: Winston Donny
Published: September 2023

When writing a multiline data structure literal, the usual convention is to put delimiters like commas at the end of each line.
Crossing the Inter-Lab Chasm
Authors: Winston Donny
Published: September 2023

Your electronic lab notebook (ELN) and/or laboratory  1  information management system (LIMS)  2  embodies ideals in various implicit or explicit forms: data formats and validators, software transformation functions and tests, planning/recording/reporting document templates, etc. Are these ideals siloed in your ELN/LIMS, or are they shared? If so, how, and is sharing robust?
A Phase Space of Reproducibility
Authors: Winston Donny
Published: September 2023

What does “reproducible science” encompass? A tug-of-war Here is one decomposition into “repeatability”, “reproducibility”, and “replicability”:  1  Here is a conflicting account of the relationship between “replicability” and “reproducibility”:  2  It seems that ACM’s “replicability” is Edward Raff’s “reproducibility”, and vice versa.
FAIR Principle R1.1: Meta(data) are released with a clear and accessible data usage license
Authors: Winston Donny
Published: September 2023

I’ve been recording introductions to each of the 15 FAIR Principles and releasing them as episodes of my Machine-Centric Science podcast (https://podcast.polyneme.xyz/). I just released the 13th one, featuring an overview of various data and code licenses. Listen here. Full transcript below (but also linked to via the episode landing page): ====== Hello, and welcome to Machine-Centric Science.
How does methane invert (its configuration)?
Authors: Rzepa Henry
Published: September 2023

This is a spin-off from the table I constructed here for further chemical examples of the classical/non-classical norbornyl cation conundrum. One possible entry would include the transition state for inversion of methane

via

a square planar geometry as compared with

e.g.

NiH

4

for which the square planar motif is its minimum.
W3C data recommendations -- there are many!
Authors: Winston Donny
Published: September 2023

The World Wide Web Consortium (W3C) publishes a range of specifications and guidelines which help move web standards forward. However, even when restricting scope to the Latest version of specifications with the status Recommendation and with the tag Data, there are currently 77 of them: https://www.w3.org/TR/?tag=data&status=REC&version=latest!
Where next for BHL?
Authors: Page Roderic
Published: September 2023

It's Friday, so time for either a folly or a rant. BHL have put another user survey into the field http://www.surveymonkey.com/s/BHLsurvey. I loathe user surveys.
Visual analysis of GBIF data
Authors: Page Roderic
Published: September 2023

Tim Roberston and the ream at GBIF are working on some nice visualisations of GBIF data, and have made an early release available for viewing: http://analytics.gbif-uat.org.
When evolution just gives up, part 5
Authors: Taylor Mike
Published: September 2023

For reals, tho,  Megatherium  , why do you even?   doi:10.59350/6meje-8zj35
DIKW Bases and Products
Authors: Winston Donny
Published: September 2023

“Self-describing” data products include/contain/link to any “knowledge products” (schema, ontology, etc.) they were informed by. In the sense of the data-information-knowledge-wisdom (DIKW) conceptualization, are there  information products  ? Perhaps self-describing  information products  include/contain/link to any “wisdom products” (usage context!
Homonyms and uBio's data model (yet more on names)
Authors: Page Roderic
Published: September 2023

As part of the TreeBASE name mapping exercise, I've come across some interesting names, such as "Diplura". This is a homonym, meaning that more than one taxon has this name. This can complicate life somewhat.
The World of Blocks
Authors: Winston Donny
Published: September 2023

Imagine a child playing with blocks. Imagine the child’s mind contains a host of smaller minds - “agents”. Imagine an agent called  Builder  in control.  Builder  makes towers from blocks:  Builder  is a simple agent.
PageRank of Linked Open Vocabularies (LOV)
Authors: Winston Donny
Published: September 2023

Datasets are easier to reuse if they use standards that are well-established, particularly in a given domain. A first approach is to ask around – ask people with whom you coauthor , people you trust in your field, etc. A follow-on approach is to examine the “graph reputation” of relevant standards, particularly if they may be represented as resources with outbound links.
No-one better tell ME giraffes aren’t all about the high browsing
Authors: Taylor Mike
Published: September 2023

On Thursday, I took the family to the Cotswolds Wildlife Park, a rather lovely zoo just over an hour away from us in Burford, Oxfordshire. Somehow I’d never even heard of this place until we passed a sign for it on the A417 a few weeks ago.
Rate of description of new animal species and *that* Taxatoy graph
Authors: Page Roderic
Published: September 2023

As part of the discussion on whether legacy biodiversity literature matters a graph from the following paper came up:So, why is the Sarkar et al. graph bogus? Here is their graph (Fig. 3) for animals:This is the number of new animal species described each year, estimated by parsing taxonomic names and extracting the date in the taxonomic authority. There are two prominent "spikes" which are worrying.
The conformation of enols: revealed and explained.
Authors: Rzepa Henry
Published: September 2023

Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation.
The ten-electron homologue of semibullvalene.
Authors: Rzepa Henry
Published: September 2023

Semibullvalene is a molecule which undergoes a facile [3,3] sigmatropic shift. So facile that it appears this equilibrium can be frozen out at the transition state if suitable substituents are used. This is a six-electron process, which leads to one of those homologous questions; what happens with ten electrons? A 5,5 double Möbius sigmatropic rearrangement. Click for 3D model.
Core Versus Crust
Authors: Winston Donny
Published: September 2023

The art of a great painting is not in any one idea, nor in a multitude of separate tricks for placing all those pigment spots, but in the great network of relationships among its parts. Similarly, the collection of data and code that comprise a digital resource are by themselves as valueless as aimless, scattered daubs of paint. What counts is what we make of them, in operational and functional phases of processes in systems.
The di-anion of dilithium (not the Star Trek variety): Another “Hyper-bond”?
Authors: Rzepa Henry
Published: September 2023

Early in 2011, I wrote about how the diatomic molecule Be

2

might be persuaded to improve upon its normal unbound state (bond order ~zero) by a double electronic excitation to a strongly bound species.
VertNet starts issue tracking using GitHub
Authors: Page Roderic
Published: September 2023

VertNet has announced that they have implemented issue tracking using GitHub. This is a really interesting development, as figuring out how to capture and make use of annotations in biodiversity databases is a problem that's attracting a lot of attention.
BioNames one year on
Authors: Page Roderic
Published: September 2023

It is almost a year to the day that I released BioNames, a database of "taxa, texts, and trees". This project was my entry in EOL's Computable Data Challenge.
Megascience platforms for biodiversity information: what's wrong with this picture?
Authors: Page Roderic
Published: September 2023

The journal  Mycokeys  has published the following paper:This paper contains a diagram that seems innocuous enough but which I find worrying:The nodes in the graph are "biodiversity megascience platforms", the edges are "cross-linkages and data exchange". What bothers me is that if you view biodiversity informatics through this lens then the relationships among these projects becomes the focus.
Edición y comunicación de la ciencia está en Rouge Scholar
Authors: Fernández Norbisley
Published: September 2023

 Hablemos de visibilidad real  En otros posts he abordado la importancia de publicar con DOI y las formas de obtenerlo. Hoy me ha llegado una noticia hermosa y al calor del júbilo esbozo estas letras.
I misconstrued the review history of the paper discussed in the last post: my apologies
Authors: Taylor Mike
Published: September 2023

Two days ago, I wrote about what seemed to be an instance of peer review gone very wrong. I’ve now heard from two of the four authors of the paper and from the reviewer in question — both by email, and in comments on the original post — and it’s apparent that I misinterpreted the situation.
Biodiversity Heritage Library blog - look but don't touch
Authors: Page Roderic
Published: September 2023

Added the Biodiversity Heritage Library blog to my links on my blog, then noticed that BHL have disabled comments. So, we can view their progress, but can't leave comments. Sigh, I wonder whether BHL has quite grasped that one of the best uses of a blog is to interact with the people who leave comments, in other words, have a conversation.
Hallucinating Datasets Across Epochal Time
Authors: Winston Donny
Published: September 2023

“Dataset” is a derived notion, a psychological construct, where “versions” of the dataset are a succession of values that we perceive to be causally related. “Dataset” is a side effect.
Adding Solr to BioStor: searching for real
Authors: Page Roderic
Published: September 2023

Prompted by the appearance on the BHL blog of an article about BioStor I've thinking about how to improve what is basically a fairly clunky tool.One major weakness is searching the collection of nearly 40,000 articles extracted from BHL. Note the word "extracted." BioStor isn't a tool like PubMed or Google Scholar where the goal is to find articles on a topic.
σ or π? The ambident nucleophilic reactivity of imines: crystallographic and computational reality checks.
Authors: Rzepa Henry
Published: September 2023

Nucleophiles are species that seek to react with an electron deficient centre by donating a lone or a π-bond pair of electrons. The ambident variety has two or more such possible sources in the same molecule, an example of which might be hydroxylamine or H

2

NOH.
Why Is There Not Just One Metadata Format for All Kinds of Research Data?
Authors: Winston Donny
Published: September 2023

Metadata modeling and formatting are separate concerns. It is reasonable that different scientific domains and studies within domains may have widely varying modeling concerns. Controlled vocabulary terms, validity constraints, and other metadata elements will surely vary and evolve over time. What’s not as obvious is why different scientific domains and studies within domains would have different formatting concerns.
Microbiome as climate, macrobiome as weather, and a global model of biodiversity
Authors: Page Roderic
Published: September 2023

Half-baked idea time. Thinking about projects such as the Earth Microbiome Project and Genomic Observatories, the recent GBIC2012 meeting (I'm still digesting that meeting), and mulling over the book A Vast Machine I keep thinking about the possible parallels between climate science and biodiversity science.
Folksonomies - why philosophy is a bad thing
Authors: Page Roderic
Published: September 2023

The November 2006 issue of D-Lib magazine contains an article by Elaine Peterson entitled "Beneath the Metadata: Some Philosophical Problems with Folksonomy" (doi:10.1045/november2006-peterson). She writes:This article is one of the most  irritating  things I've read in a while, and as much as I like philosophy, it reinforces my prejudice that invoking philosophy is almost always a bad idea.
Here’s that hen respiratory system segmentation you ordered
Authors: Taylor Mike
Published: September 2023

Two and a half years ago, I posted a glorious hemisected hen, taken (with permission) from a poster by Roberts et al. 2016, and supplied by Ray Wilhite, best known in this parish for his work on sauropod appendicular material. At the end of that post, I blithely promised “More from this poster in a subsequent post!”, and then — predictably — forgot all about it. My apologies.
¬ consistent ⇒ ¬ valid ⇒ ¬ accurate
Authors: Winston Donny
Published: September 2023

If it’s not consistent, it can’t be valid. If it’s not valid, it can’t be accurate. If it’s not accurate, who cares if it’s timely? Subscribe to get short notes like this on Machine-Centric Science delivered to your email.
The impact of museum collections: one collection ≈ one Nobel Prize
Authors: Page Roderic
Published: September 2023

Ideas on measuring the "impact" of a natural history collection have been bubbling along, as reflected in recent comments on iPhylo, and some offline discussions I've been having with David Blackburn and Alan Resetar.My focus has been at the specimen-level, with a view to motivation the adoption of persistent specimen-level identifiers so that we can citations of specimens over time (e.g., in publications and databases such as GenBank). Not only
Generalizing the Postdoc Position
Authors: Winston Donny
Published: September 2023

A traditional postdoc filler seeks to transition to a different role, that of professor or staff. What if someone were to  specialize  in this kind of role, e.g. for a certain kind of project in a certain kind (e.g. group size) of research environment? Such a position would be akin to the modern \(\approx\) 1-3 yr startup position specialized to a certain growth stage of a startup.
Brachiosaurus altithorax, mounted inside the Field Museum, redux
Authors: Taylor Mike
Published: September 2023

I have often lamented that there are so very few photos of the Field Museum’s  Brachiosaurus  mount from that brief six years — 1993 to 1999 — when it was the centrepiece of the main hall. It seems to have been kicked out just a year or two too early to get captured by numerous digital cameras.
Software User Facilities
Authors: Winston Donny
Published: September 2023

There are user facilities for scientific research. They were born out of the cost of doing “big science” with hardware that was increasingly resource-intensive, in terms of physical space, personnel time, and materials. Lawrence’s first cyclotron fit in the palm of his hand. Then he needed the hills behind Berkeley’s university campus.
Agents and Agencies
Authors: Winston Donny
Published: September 2023

We want to explain complicated things as a combination of simpler things. You must be prepared to feel a certain sense of loss. When we break things down to their smallest parts, they may each seem as dry as dust at first, as though some essence has been lost. Where does the “knowing-how-to-build” of a  Builder  agent reside? It is not in any part, so it is not enough to explain what each separate agent does.
Rethinking citation matching
Authors: Page Roderic
Published: September 2023

Some quick half-baked thoughts on citation matching. One of the things I'd really like to add to BioStor is the ability to parse article text and extract the list of literature cited.
Are People Machines?
Authors: Winston Donny
Published: September 2023

Are people machines? “Everyone knows that machines can behave only in lifeless, mechanical ways.” This objection seems reasonable. A person ought to feel offended at being likened to any  trivial  machine. But it seems to me that the word “machine” is getting to be out of date. We ought to recognize that we’re still in an early era of machines, with virtually no idea of what they may become.
Data Stacks for FAIR
Authors: Winston Donny
Published: September 2023

I noticed a pattern at the top of each case study listed by Stemma.ai, which provides data catalog software as a service based on the open-source Amundsen code. Each case study’s so-called “Data Stack” comprises up to four distinct categories of functionality – Data Catalog, Data Warehouse, ETL, and Business Intelligence.
CrossRef's OpenURL resolver
Authors: Page Roderic
Published: September 2023

CrossRef's OpenURL resolver can be used to find DOIs for papers, or give a DOI it can extract metadata.
Open course on phyloinformatics
Authors: Page Roderic
Published: September 2023

As part of a postgraduate course here at the University of Glasgow I'm teaching five sessions on "phyloinformatics", which I've decided to define broadly enough to encompass most of biodiversity informatics.Given that this module is being developed on the fly, and will make use of lots of little "toys" I've developed and discussed on this blog, I've decided to put the course notes online, along with the interactive demos and the source code.
Place Oriented Publishing Versus Value Oriented
Authors: Winston Donny
Published: September 2023

In place-oriented publishing, as in place-oriented programming, you allocate places to push things, and you pull from places. Places steward values. “Where” something is, is important. Did you publish to a reputable place? In value-oriented publishing, as in value-oriented programming, you pass around values, or references to values, not to places. You deal directly in values. Dereferencing services steward values.
Novelists and Reductionists
Authors: Winston Donny
Published: September 2023

Some like to focus on the new. They like to invent theories. Some are adamant about reducing to what has come before. This has worked remarkably well for the core of physics. These inclinations are not incompatible given some kind of “leveling”, with discipline about connections. Standing on the shoulders of giants and all that. Much of apparent “novelty” may be reducible to the structured annotation and (re-)configuration of core mechanism.
David Shorthouse enters the blogsphere
Authors: Page Roderic
Published: September 2023

David Shorthouse has entered the blogsphere with his iSpiders blog.
What's Inside the Arrows?
Authors: Winston Donny
Published: September 2023

Inside black boxes you find programs. There are a lot of programming languages. You may not care how black box \(A\) works as a substitute for black box \(B\) if it’s observationally equivalent to black box \(B\). How do the boxes interact? What’s inside the arrows that connect the boxes? Inside arrows you find protocols. There are a lot of protocols.
GSC23: Talking standards in Bangkok
Authors: Hunter Chris
Published: September 2023

The GSC23 international meeting was held in Bangkok, Thailand earlier this month (Aug 7-11th) and here we have an overview of this meeting. The Genomic Standards Consortium (GSC) is a volunteer-run non-profit organization set up nearly 20 years ago. At a time when “genomic” researchers were painstakingly producing near-complete genomes of just a few organisms.
What Functions Do Ideas About Selves Serve?
Authors: Winston Donny
Published: September 2023

One must not mistake defining things for knowing what they are. You can know what a tiger is without defining it. You may define a tiger, yet know scarcely anything about it. “Self” is a term used to talk about a sense of identity.
More GBIF specimen identifier strangeness
Authors: Page Roderic
Published: September 2023

Continuing the theme of trying to map specimens cited in the literature to the equivalent GBIF records, consider the GBIF record http://data.gbif.org/occurrences/685591320, which according to GBIF is specimen "ZFMK 188762" (a [sic] holotype of  Praomys hartwigi  ).This is odd, because the original publication of this name (Eisentraut, M. 1968 .Beitrag zur Saugetierfauna von Kamerun.
Holes and Parts
Authors: Winston Donny
Published: September 2023

What keeps a mouse contained in a box? It is the way a box prevents motion in all directions. Each board bars escape in a certain direction. The left side keeps the mouse from going left, the right from going right, the top keeps it from leaping out, and so on. The secret of a box is simply in how the boards are arranged to prevent motion in  all  directions. That’s what  containing  means.
Column-Name Contracts
Authors: Winston Donny
Published: September 2023

URIs are great for namespacing terms. However, the local names — after the last / — could be a free-for-all. One common convention — but not typically a  contract  — is to use upper camel case for rdfs:Class instances and lower camel case for rdf:Property instances. Is it useful to systematize the construction of local names? Emily Riederer argues yes.
Migrating Conflicts Between Agents to Higher Levels
Authors: Winston Donny
Published: September 2023

Many children not only like to build, they also like to knock things down – to hear the complicated noises and watch so many things move at once. Let’s imagine a sibling agent to  Builder  called  Wrecker  , whose specialty is knocking things down: Suppose  Wrecker  gets aroused, but there’s nothing in sight to smash. Then  Wrecker  will have to get some help – by putting  Builder  to work, for example.
A Sign Helps You Use It as Though It Were an X
Authors: Winston Donny
Published: September 2023

For evolvable data exchange, you need to be able to continually add qualified references galore so that participants can reason by analogy – i.e., each new thing resembles something known before. This is FAIR principle I3, which depends on I1 and I2 for robustness. Subscribe to get short notes like this on Machine-Centric Science delivered to your email. M. Minsky,  The Society of Mind  . New York: Simon and Schuster, 1986, p.
A Flexible Schema is Like a Rubber Ruler
Authors: Winston Donny
Published: September 2023

It is better to have a large variety of firm rulers that feed into selection pressure for utility in some environment, than to have a few flexible ones for which your measurements aren’t consistent. Generate and test. Conjecture and refute. May there be a flowering of crisp attribute and entity specs. A flexible schema is like a rubber ruler.
Using Google Refine and taxonomic databases (EOL, NCBI, uBio, WORMS) to clean messy data
Authors: Page Roderic
Published: September 2023

Google Refine is an elegant tool for data cleaning. One of its most powerful features is the ability to call "Reconciliation Services" to help clean data, for example by matching names to external identifiers. Google Refine comes with the ability to use Freebase reconciliation services, but you can also add external services.
One Self or Many
Authors: Winston Donny
Published: September 2023

Is a self a centralized entity? Is it a society that includes both images of what is (“data”) and ideals about what ought to be (“schema”)? Sometimes we feel decentralized or dispersed, as though we were made of many different parts with different tendencies:  “One part of me wants this, another part wants that. 
Mean-ing
Authors: Winston Donny
Published: September 2023

A mean is a central tendency or location. Examples include arithmetic and geometric means. A distribution can have a strong or weak central tendency, that is, a small or large dispersion, respectively.
processing PhylOData (pPOD)
Authors: Page Roderic
Published: September 2023

Some good news! pPOD, a NSF-funded project on integrating data from AToL (A Tree of Life) projects has been funded. Val Tannen (right) is the co-ordinating PI. I'm a consultant, which means more opportunities to mouth-off about phylogenetic data and databases (for earlier examples see TreeBASE rocks, TreeBASE talk at CIPRES, and Towards the ToL database - some visions).The project is called pPOD, and has a wiki.
Hierarchies, Heterarchies, and Agent Memory
Authors: Winston Donny
Published: September 2023

In a hierarchy, each agent only acts on behalf of one other agent: from rdflib import Graph from rdflib.namespace import RDF, PROV def hierarchy(graph): return all( len(set(graph.objects(agent, PROV.actedOnBehalfOf))) <= 1 for agent in graph.subjects(RDF.type, PROV.Agent) ) hierarchy(Graph().parse(data=""" @prefix prov: . @prefix : . :doc a prov:Agent; . :sleepy a prov:Agent;
Biodiversity informatics in charts
Authors: Page Roderic
Published: September 2023

I've just come back from II Iberian Congress of Biological Systematics (CISA2013) in Barcelona, where I had a great time.
Request Your Cake and Eat It Too
Authors: Winston Donny
Published: September 2023

I was alerted to a great discussion  1  about unifying versus partitioning data models. That is, you have some data powering some part of your system, and you need to decide how to structure that data and associate validation logic and behavior – like calculating properties or triggering other system actions – with the bundle of data as it evolves over the course of some ongoing or completing process.
These are my species - finding the taxonomic names I published using Mendeley
Authors: Page Roderic
Published: September 2023

The latest addition to my mapping of taxonomic names to the literature (http://iphylo.org/~rpage/itaxon/) is the ability for authors with Mendeley accounts to find the names they've published. This is an extension of the "I wrote that" tool I developed earlier.Let's say I want to show the names that a given author has published.
Re-implementing the upload of images for the LaTeX→HTML converter
Authors: Willighagen Lars
Published: September 2023

The CDLI is developing a new website. That website’s admin interface for its journals contains a page where a LaTeX source file, following a specific template, is configured to an HTML page. For this, apart from the LaTeX file itself, two additional components are needed: a BibTeX file, containing metadata of the references; and image files.
"We Need to Dockerize and Distribute Robert"
Authors: Winston Donny
Published: September 2023

Design is taking things apart in order to be able to put them back together.  2  You must  design  the digital resources you archive and disseminate, so that you don’t “need to dockerize and distribute Robert” (overheard in a Slack room), which, of course, you can’t. Subscribe to get short notes like this on Machine-Centric Science delivered to your email.
GUIs and APIs Are Both Human Interfaces
Authors: Winston Donny
Published: September 2023

GUIs and APIs are both human interfaces. They both frame perspectives on data/operation service offerings so that human beings can navigate and consume them. The human being in the case of APIs is the application programmer, a subset of users. GUIs are applications, so it is natural to expect an API’s capabilities to be a superset of a corresponding GUI’s — application programmers program the GUI using the API.
Screening for Generality: Reflections
Authors: Wagen Corin
Published: September 2023

Now that our work on screening for generality has finally been published in Nature, I wanted to first share a few personal reflections and then highlight the big conclusions that I gleaned from this project.
Reflections on the TDWG RDF "Challenge"
Authors: Page Roderic
Published: September 2023

This is a follow up to my previous post TDWG Challenge - what is RDF good for? where I'm being, frankly, a pain in the arse, and asking why we bother with RDF? In many ways I'm not particularly anti-RDF, but it bothers me that there's a big disconnect between the reasons we are going down this route and how we are actually using RDF.
Names and nomenclators: just do it already!
Authors: Page Roderic
Published: September 2023

Quick notes on taxonomic names (again). It's a continuing source of bafflement that the biodiversity community is making a dog's breakfast of names. It seems we are forever making it more complicated than it needs to be, forever minting new acronyms that pollute the landscape without actually contributing anything useful, and forever promising shiny new tools and services without every actually delivering them.
Data Ventriloquy
Authors: Winston Donny
Published: September 2023

Who’s the last ventriloquist when it comes to a dataset? You pull data and accrete it with other data, reshape it, and reduce it, and ultimately make it dance and speak via structured representation, software action, narrative exposition, etc. Can someone further contribute to the life journey of that processed data, repurposing your representation, inserting their arm to make an adjustment with a tool of their choice?
Wholes and Parts, in FAIR and Mind
Authors: Winston Donny
Published: September 2023

It is the nature of FAIR that can make digital resources kin – interoperable in fugues of machine action. The differences in the schema, serialization, or domain-specificity of the digital datoms out of whose intricate relationships any given resource is built are altogether trivial. Subscribe to get short notes like this on Machine-Centric Science delivered to your email.
Organocatalytic cyclopropanation of an enal: (computational) mechanistic understanding.
Authors: Rzepa Henry
Published: September 2023

Symbiosis between computation and experiment is increasingly evident in pedagogic journals such as

J. Chemical Education

. Thus an example of original laboratory experiments[cite]10.1021/ed077p271[/cite],[cite]10.1021/ed078p1266[/cite] that later became twinned with a computational counterpart.[cite]10.1021/ed500398e[/cite] So when I spotted this recent lab experiment[cite]10.1021/acs.jchemed.7b00566[/cite] I felt another twinning
BioNames: yet another taxonomic database
Authors: Page Roderic
Published: September 2023

Yet another taxonomic database, this time I can't blame anyone else because I'm the one building it (with some help, as I'll explain below).BioNames was my entry in EOL's Computable Data Challenge (you can see the proposal here: http://dx.doi.org/10.6084/m9.figshare.92091). In that proposal I outlined my goal:The bulk of the funding from EOL is going into interface work by Ryan Schenk (@ryanschenk), author of synynyms among other cool things.
Why Publishing Failures is Important for Science
Authors: Winston Donny
Published: September 2023

Not documenting failures causes them to be repeated. This repetition is waste because no new information is generated. Only  new  failures generate information. There is an optimum failure rate.  1  We can avoid oversimplifications like “embrace failures” or “avoid failures”. We maximize information gain by making outcomes equally likely. Thus, for a test with two outcomes, seek a 50% failure rate.
The Principle of Noncompromise
Authors: Winston Donny
Published: September 2023

Whenever several agents have to compete for the same resources, they are likely to get into conflicts. Those agents’ superiors, too, may be under competitive pressure and likely to grow weak themselves whenever their subordinates are slow in achieving their goals, no matter whether because of conflicts between them or because of individual incompetence.
Timescales
Authors: Wagen Corin
Published: September 2023

For many organic chemists, it’s hard to grasp the vast difference between various “fast” units of time.
Automatic RSS Feed for Each Tag in a Hugo Blog
Authors: Winston Donny
Published: September 2023

This is a test to see if tag-specific RSS feeds are automatically generated for each tag in a Hugo blog. The front matter for this post is: --- title: "Automatic RSS Feed for Each Tag in Hugo" date: 2021-09-03T09:33:37-04:00 draft: false tags: - test --- Woohoo! /tags/test/index.xml was automatically created on deploy!
Site-Selective Glycosylation: Reflections
Authors: Wagen Corin
Published: September 2023

Now that our lab’s site-selective glycosylation has been published, I wanted to share some reflections from the computational portion of the work.
GBIF and open biodiversity data: what license should GBIF use?
Authors: Page Roderic
Published: September 2023

GBIF is asking for views on how it should license of data in the GBIF network. The full consultation document is available from Google Drive and DropBox.
In defence of OpenURL: making bibliographic metadata hackable
Authors: Page Roderic
Published: September 2023

This is not a post I'd thought I'd write, because OpenURL is an awful spec. But last week I ended up in vigorous debate on Twitter after I posted what I thought was a casual remark:This ended up being a marathon thread about OpenURL, accessibility, bibliographic metadata, and more.
Let Traits Accrete
Authors: Winston Donny
Published: September 2023

How can it be that complex, dynamic objects can be described by short and simple strings and words? We often seek:  1   Selectivity  – Our images are often falsely clear. We may think of an object’s “personality” in terms of that which we can easily describe. We may set aside the rest for now as though it simply weren’t there.
BioNames update - matching taxon names to classifications
Authors: Page Roderic
Published: September 2023

On eof the things BioNames will need to do is match taxon names to classifications. For example, if I want to display a taxonomic hierarchy for the user to browse through the names, then I need a map between the taxon names that I've collected and one or more classifications. The approach I'm taking is to match strings, wherever possible using both the name and taxon authority.
Parts and Wholes
Authors: Winston Donny
Published: September 2023

What makes a tower more than separate blocks, or a wall more than a set of many bricks? Every block/brick is held in place by its neighbors and gravity. Why is a chain more than its various links? To explain why chain-links cannot come apart, we can demonstrate how each would get in its neighbors’ way. In graphical diagrams of such physical situations, the edges drawn between nodes are – implicitly or explicitly – labeled, qualified relations.
Schemes for Indirect Control
Authors: Winston Donny
Published: September 2023

There are two fundamental approaches to indirect control in code.  1  In an  open  approach, we can change the behavior of dereferencing code by conveying different values. The decision-making mechanism must be unordered.
Lean Web - Principles of Lean Thinking applied to Web Development
Authors: Winston Donny
Published: September 2023

Lean manufacturing aims to reduce waste in production processes and to reduce response times to consumers from producers. Womack and Jones  1  authored five key principles for lean thinking in the context of manufacturing:  Value  : Identify the value of a product to a consumer.  Value Stream  - Identify the minimal process (steps, time, information, material) to produce the value.
Metadata as Relations Between Identifiers
Authors: Winston Donny
Published: September 2023

With linked data, then, Consider that in RDF, even literals are objects.
The Persistence of Identity
Authors: Winston Donny
Published: September 2023

What is that strange possession that stays the same throughout its life?  1  Can we recollect how things appeared to us before we learned to link new meanings to those things? What is this body of changelessness in spite of change?
Mapping evolutionary biology: @evoldir and #ProjectEvoMap
Authors: Page Roderic
Published: September 2023

Robert M. Griffin (@GriffinEvo) has launched ProjectEvoMap. Rob explains:Below is a screen shot of part of the map.
Ensure That Provenance Bottoms Out
Authors: Winston Donny
Published: September 2023

Some questions may be pursued circularly, where for example you cannot find a final cause – you must ask,  What caused that cause?  Or you cannot find an ultimate goal –  Then what purpose does  that  serve?  Such loops can waste our time.  1  It is a form of self-control to establish ways to bottom out, to employ base cases to stop recursion.
Molecules of the year? The most polar neutral compound synthesized…
Authors: Rzepa Henry
Published: September 2023

This, the fourth candidate provided by C&EN for a vote for the molecule of the year as discussed here, lays claim to the World’s most polar neutral molecule (system

1

shown below).[cite]10.1002/anie.201508249[/cite] Here I explore a strategy for extending that record.
Bat names, ligatures, and fonts
Authors: Page Roderic
Published: September 2023

Notes on fonts in trying decipher some bat names (and sort out some synonyms). It can be difficult to tell "œ" (o + e) from "æ" (a + e) in some texts.
EOL challenge draft proposal
Authors: Page Roderic
Published: September 2023

In the spirit of the Would you give me a grant experiment? [1] here's the draft of a proposal I'm working on for the Computable Data Challenge. It's an attempt to merge taxonomic names, the primary literature, and phylogenetics into one all-singing, all-dancing website that makes it easy to browse names, see the publications relevant to those names, and see what, if anything, we know about the phylogeny of those taxa.
Google, the Ken Burns Effect, and Fractal Cognitive Engagement
Authors: Page Roderic
Published: September 2023

From One Big Library, a nice screencast of why Google's interface works, in contrast to the clunky interfaces favoured by libraries (and databases such as TreeBASE). (If you don't see the video here, visit http://www.youtube.com/watch?v=ijLDxgALc2c.)
Google doesn't like BioStor anymore
Authors: Page Roderic
Published: September 2023

According to Google Analytics BioStor has experienced a big drop in traffic since the start of October:At one point I'm getting something like 4500 visits a week, now it's just over a thousand a week. I'm guessing this is due to Google's 'Panda' update. I suspect part of the problem is that in terms of text content BioStor is actually pretty thin.
Catalogue of Life and LSIDs: a catalogue of fail
Authors: Page Roderic
Published: September 2023

I have a love/hate relationship with the Catalogue of Life (CoL). On the one hand, it's an impressive achievement to have persuaded taxonomists to share names, and to bring those names together in one place. I suspect that Frank Bisby would feel that the social infrastructure he created is his lasting legacy.
The π-π stacking of aromatic rings: what is their closest parallel approach?
Authors: Rzepa Henry
Published: September 2023

Layer stacking in structures such as graphite is well-studied. The separation between the π-π planes is ~3.35Å, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7Å). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen bonding can contract the vdW distance sum by up to ~0.8Å or even more?
Flow and Meaning
Authors: Winston Donny
Published: September 2023

I recently came across a procedure for achieving a flow state: One activity at a time. The activity is meaningful to you. You work at the edge of your abilities. I can’t recall the source of this. So, dear reader, please send me something I can cite if you have encountered this 3-step procedure elsewhere. In this post, I relate the above procedure to my recent post on mean-ing.
Directness Is Dangerous
Authors: Winston Donny
Published: September 2023

If self-control were easy, we might end up accomplishing nothing at all. Extinction would be swift indeed for species that could simply switch off hunger or pain. Instead, there must be checks and balances. Imagine if any one process could seize and hold control over all the rest – we wouldn’t complete many tasks. So, for processes to exploit each other’s skills, roundabout pathways have to be discovered. Fantasies can provide missing paths.
Data, Information, Knowledge, Wisdom (DIKW)
Authors: Winston Donny
Published: September 2023

The DIKW  1  decomposition expresses a layering of context on top of raw observations. Data points are attributes – components of facts. They are actuals (e.g., measured numbers) that can be connected to contexts. Information is data tied to context, i.e. processed data (“history”) that reduces uncertainty wrt what, when, where, and who.
Reasoning Lets You See What Isn't There
Authors: Winston Donny
Published: September 2023

What is the “killer use case” for Reasoning, i.e., inferencing over a semantic graph database? Data in a relational database “knows nothing.” Data in a graph database “knows how it is connected” – you can ask an entity to tell you who its neighbors are 3 hops out, or if two pieces are connected up to 20 hops. Data with Reasoning “knows how to think.” But what does that mean exactly? What do you get?
Sending Signal-Signs
Authors: Winston Donny
Published: September 2023

Sending signal-signs  1  to steer engines of compute, the wheel does no work. Subscribe to get short notes like this on Machine-Centric Science delivered to your email.
Document layout analysis
Authors: Page Roderic
Published: September 2023

How to cite:

Page, R. (2023). Document layout analysis. https://doi.org/10.59350/z574z-dcw92

Some notes to self on document layout analysis. I’m revisiting the problem of taking a PDF or a scanned document and determining its structure (for example, where is the title, abstract, bibliography, where are the figures and their captions, etc.). There are lots of papers on this topic, and lots of tools.
Components and Connections
Authors: Winston Donny
Published: September 2023

An agent like  Builder  is not merely a collection of parts like  Find  ,  Get  ,  Put  , and all the rest.  Builder  would not work at all unless those agents were linked to one another by a suitable network of interconnections: Could you predict what  Builder  does from knowing just that left-hand list above? Of course not. First, we must know how each separate part works.
Slot Long Range Plans Into Ecosystems
Authors: Winston Donny
Published: September 2023

A principled system has predictable relationships between its modules, whereas an adaptable system has sparse and flexible relationships between its modules.
The Curtius rearrangement. One step or two?
Authors: Rzepa Henry
Published: September 2023

The Curtius reaction is represented in most chemistry texts and notes as following path (a) below. It is one of a general class of thermally induced rearrangement which might be described as elimination/migration (in a sense similar to this ring contraction migration/elimination), in this case implicating a nitrene intermediate if the two steps occur consecutively.