Rants, raves (and occasionally considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics.  For more ranty and less considered opinions, see my Twitter feed.ISSN 2051-8188. Written content on this site is licensed under a Creative Commons Attribution 4.0 International license.

University of Glasgow

For a while now I’ve been exploring ways to navigate through DNA barcodes. Over the years I’ve built various “toys” to explore barcodes, such as Displaying a million DNA barcodes on Google Maps using CouchDB, built a small scale browser using Elastic search that had some succes, and discovered that Postgres can search for DNA sequences and it’s really fast.

BOLD View: exploring DNA barcodes

Quick final comment on the TDWG Challenge - what is RDF good for?. As I noted in the previous post, Olivier Rovellotti (@orovellotti) and Javier de la Torre (@jatorre) have produced some nice visualisations of the frog data set:Nice as these are, I can't help feeling that they actually help make my point about the current state of RDF in biodiversity informatics.

Final thoughts on TDWG RDF challenge

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.

processing PhylOData (pPOD)

For the "to do" list, expand-ahead browsing looks like a useful approach to build upon PygmyBrowse (see my live demo). The approach is described in "Expand-Ahead: A Space-Filling Strategy for Browsing Trees" by McGuffin et al. (doi:10.1109/INFOVIS.2004.21, PDF also here).  There is a video on Ravin Balakrishnan's site, which is an AVI file that I haven't bee able to coerce my Mac into playing, hence I've posted it on YouTube.

Expand-Ahead: A Space-Filling Strategy for Browsing Trees

Following on from the previous post, as Howison and Goodrum note, Adobe provides XMP as a way to store metadata in files, such as PDFs. XMP supports RDF and namespaces, which means widely used bibliographic standards such as Dublin Core and PRISM can be embedded in a PDF, so the article doesn't become separated from its metadata. Adobe provides a developers kit under a BSD license.

How to cite:

 Page, R. (2024). Exploring BOLD's DNA barcode data releases: there's a fraction too much friction https://doi.org/10.59350/6qepn-ge510

Recently I’ve been exploring data downloaded from BOLD. Part of this was motivated by work done with David Schindel for a recent book: In this blog post I record some struggles I’ve had with the supposedly “Frictionless” data provided by BOLD.

Exploring BOLD's DNA barcode data releases: there's a fraction too much friction

Quick note on a tool I've been working on to parse citations, that is to take a series of strings such as: Möllendorff O (1894) On a collection of land-shells from the Samui Islands, Gulf of Siam. Proceedings of the Zoological Society of London, 1894: 146–156. de Morgan J (1885) Mollusques terrestres &amp; fluviatiles du royaume de Pérak et des pays voisins (Presqúile Malaise). Bulletin de la Société Zoologique de France, 10: 353–249.

Citation parsing tool released

The IEEE SMC Society's eNewsletter has short article on work in Jason Wang's group on struture-base queries.

Structural-based queries

I'm going to the TDWG Identifier Workshop this weekend, so I thought I'd jot down a few notes.

On identifiers (again)

I've uploaded all the COI barcodes in the iBOL public data dumps into GBIF. This is an update of an earlier project that uploaded a small subset. Now that dataset doi:10.15468/inygc6 has been expanded to include some 2.7 million barcodes.

iBOL DNA barcodes in GBIF

Browsing Mendeley I found the following record: http://www.mendeley.com/research/description-larva/. This URL is for a paperwhich apparently has the DOI doi:10.1645/GE-2580.1. This is strange because

 Zootaxa

doesn't have DOIs. The DOI given resolves to a paper in the

 Journal of Parasitology

:Now, this paper has it's own record in Mendeley.OK, so this is weird..., but it gets weirder.

Phantom articles: why Mendeley needs to make duplication transparent

One problem with my cunning plan to use Mediawiki REDIRECTs to handle DOIs is that some DOIs, such as those that BioOne serves based on SICIs contain square brackets, [ ], which conflicts with wiki syntax.

Rewriting DOIs

Continuing the series of posts about reading scientific articles on the iPad, here are some quick notes on perhaps the most polished app I've seen, Papers for iPad. As with earlier posts on the Nature and PLoS apps, I'm not writing an in-depth review - rather I'm interested in the basic interface design.Papers is available for the Mac, as well as the iPhone and iPad.

Viewing scientific articles on the iPad: Papers

Just noticed that BioStor now has just over 70,000 articles extracted from the Biodiversity Heritage Library. This number is a little "soft" as there are some duplicates in the database that I need to clean out, but it's a nice sounding number.

70,000 articles extracted from the Biodiversity Heritage Library

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

The impact of museum collections: one collection ≈ one Nobel Prize

Notes on how many georeferenced DNA sequences there are in GenBank, and how many could potentially be georeferenced.

Notes on finding georeferenced sequences in GenBank

Quick notes to self on fulltext search and CouchDB. Note that links to CouchDB are local to my machine(s),and won't work unless you are me, or have a copy of the same database running on your machine). CouchDB and Lucene adds fulltext indexing to CouchDB. After a few false starts I now have this working.

CouchDB and Lucene

My BioNames project has been going for over a year now, but I hadn't gotten around to providing bulk access to the data I've been collecting and cleaning. I've gone some way towards fixing this. You can now grab a snapshot of the BioNames database as a Darwin Core Archive here.

BioNames database can be downloaded

Dion Hinchcliffe has a piece entitled Creating real business value with Web 2.0 which lists AntBase.org (I think he actually means AntWeb) as an example of a non-commercial Web 2.0 service that demonstrates "scalable marshalling of underutilized data resources," and shows:  The article comes with this graphic:    See also Dion's Thinking in Web 2.0: Sixteen ways (via Danny Ayers).

AntBase and Web 2.0 business value

Over on the EOL blog is a summary of a meeting Visualizing the Evolutionary Tree of Life. This sounds like it was a fun meeting, but part of me is suffering from déjà vu. Our community has tossed this subject around for a while now.

Visualizing the Evolutionary Tree of Life

Reading a recent TAXACOM thread (Species Pages - purpose) my sense is that some people are arguing that "species pages" would be time consuming to create, aren't much good for taxonomists (to quote Mike Dallwitz "In brief, to make simplified and attractive information about taxa easily available to casual users?"), and nobody gets credit for making them.

Wiki demo

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, the Ken Burns Effect, and Fractal Cognitive Engagement

I think this isn't supposed to happen, but here's a paper with

 two

DOIs. The first DOI is doi:10.1651/0278-0372(1997)17[253:MPAOTC]2.0.CO;2, which links to a record served by BIOONE.

Duplicate DOIs

How to cite:

 Page, R. (2024). The Data Citation Corpus revisited https://doi.org/10.59350/wvwva-v7125

TL;DR These are some brief notes on the latest version (v. 2) of the Data Citation Corpus, relased shortly before the Make Data Count Summit 2024, which also included a discussion on the practical uses of the corpus. I downloaded version 2 from Zenodo doi:10.5281/zenodo.13376773.

The Data Citation Corpus revisited

Chris Freeland's tweet alterted me to the Elsevier Article 2.0 Contest:  Elsevier are clearly looking for ideas (they also have their Grand Challenge), and there's been some interesting commentary on the Article 2.0 contest.

Elsevier Article 2.0 Contest

Following on from adding specimens to my OpenURL resolver, I've added support for GenBank records. Either an OpenURL request such as http://bioguid.info/openurl?id=genbank:DQ502033, or the short URL http://bioguid.info/genbank/DQ502033 will resolve the GenBank record for accession number DQ502033.

OpenURL for Genbank records

A couple of articles in the tech press got me thinking this morning about Bitcoin, Ted Nelson, Xanadu, and the web that wasn't. The articles are After The Social Web, Here Comes The Trust Web and Transforming the web into a HTTPA 'database'. There are some really interesting ideas being explored based on centralised tracking of resources (including money, think Bitcoin, and other assets, think content). I wonder whether these developments may

Bitcoin, Xanadu, Ted Nelson, and the web that wasn't

There are several instances where I have a collection of references that I want to deduplicate and merge.

Deduplicating bibliographic data

Note to self (basically rewriting last year's Finding citations of specimens). Bibliographic data supports going from identifier to citation string and back again, so we can do a "round trip."

 1.

Given a DOI we can get structured data with a simple HTTP fetch, then use a tool such as citation.js to convert that data into a human-readable string in a variety of formats.

Round trip from identifiers to citations and back again

I've released a simple search engine for publications in Wikidata. Wikicite Search takes its name from the WikiCite project, which was an initiative to create a bibliographic database in Wikidata. Since bibliographic data is a core component of taxonomic research (arguably taxonomy is mostly tracing the fate of the "tags" we call taxonomic names) I've spent some time getting taxonomic literature into Wikidata.

Towards a WikiCite search engine

The following is a guest post by Bob Mesibov. The first Darwin Core Million closed on 31 March with no winner. Since I'm seeing better datasets this year in my auditing work for Pensoft, I've decided to run the competition every six months. Missed the first Darwin Core Million and don't know what it's about?

Darwin Core Million now twice a year

Somewhat stunned by the fact that my DNA barcode browser I described earlier was one of the (minor) prizewinners in this year's GBIF Ebbe Nielsen Challenge. For details on the winner and other place getters see ShinyBIOMOD wins 2020 GBIF Ebbe Nielsen Challenge. Obviously I'm biased, but it's nice to see the challenge inspiring creativity in biodiversity informatics. Congratulations to everyone who took part.

GBIF Challenge success

The following is a guest post by Bob Mesibov. The Atlas of Living Australia (ALA) adds "assertions" to Darwin Core occurrence records.

Australian museums and ALA

I'm doing some work with Nicole Kearney (@nicolekearney) at the Melbourne Museum on the general theme of "linking all the things". It's the end of the first full week we've had, so here's a quick update of what we've been up to.

 Brainstorming

The things we want to do are being captured as a project on GitHub. This is where we come up with ideas, comment on then, then try to figure out which ones can be done.

Messages from Melbourne: Towards linking all the things

I've written up my entry for the 2018 GBIF Challenge ("Ozymandias") and posted a preprint on Biorxiv (https://www.biorxiv.org/content/early/2018/12/04/485854). The DOI is https://doi.org/10.1101/485854 which, last time I checked, still needs to be registered.  The abstract appears below. I'll let the preprint sit there for a little while before I summon the enthusiasm to revisit it, tidy it up, and submit it for publication.

Ozymandias: A biodiversity knowledge graph available as a preprint on Biorxiv

While working with linked data and ways to explore and visualise information, I keep coming back to the Haystack project, which is now over a decade old. Among the tools developed was the Haystack application, which enabled a user to explore all sorts of structured data. Below is a screen shot of Haystack showing a sequence for Homo sapiens cyclin T1 (CCNT1), transcript variant a, mRNA.

Notes on collections, knowledge graphs, and Semantic Web browsers

One of the things the biodiversity informatics community has struggled to do is come up with a list of all natural history collections (Taylor, 2016). Most recently GrBio attempted to do this, and appealed for community help to curate the list (Schindel et al., 2016), but this did not emerge, and at the time of writing GrBio is moribund.

Where is the damned collection? Wikidata, GrBio, and a global list of all natural history collections

Prompted by a conversation with Vince Smith at the recent Online Taxonomy meeting at the Linnean Society in London I've been revisiting touch-based displays of large trees. There are a couple of really impressive examples of what can be done.

 Perceptive Pixel

I've blogged about this before, but came across another video that better captures the excitement of touch-based navigation of a taxonomy.

Touching the tree of life

Being in Ottawa last week for a hackathon meant I could catch up with David Shorthouse (@dpsSpiders. David has been doing some neat work on linking specimens to identifiers for researchers, such as ORCIDs, and tracking citations of specimens in the literature. David's Bloodhound tool processes lots of GBIF data for occurrences with names of those who collected or identified specimens.

Specimens, collections, researchers, and publications: towards social and citation graphs for natural history collections

I've been viewing Apple's Knowledge Navigator concept video from 1987 and it's striking how much of this we have today, and yet how far away we are from the complete vision. For some background on this promotional video see The Making of Knowledge Navigator.

Apple's Knowledge Navigator concept video (1987): we are still a long way from this vision

In preparation for WikiCite 2017 I'm looking more closely at extracting bibliographic information from Wikispecies. The WikiCite project "is a proposal to build a bibliographic database in Wikidata to serve all Wikimedia projects". One reason for doing this is so that each factual statement in WikiData can be linked to evidence for that statement.

Notes for WikiCite 2017: Wikispecies reference parsing

BioStor now has 150,000 articles. When I wrote a paper describing how BioStor worked it had 26,784 articles, so things have progressed somewhat! I continue to tweak the interface to BioStor, trying different ways to explore the articles.

 Spatial search

I've tweaked spatial search in BioStor.

BioStor updates: nicer map, reference matching service

Awoke this morning to the sad news (via Scott Miller) that Scott Federhen of the NCBI had died. Anyone using the NCBI taxonomy is a beneficiary of Scott's work on bring together taxonomy and genomic data. Scott contributed both directly and indirectly to this blog.

Scott Federhen

A decade ago (OMG, that can't be right, an actual decade ago) I created "iSpecies", a simple little tool to mashup a variety of data from GBIF, NCBI, Yahoo, Wikipedia, and Google Scholar to create a search engine for species.

iSpecies is back: mashing up species data

My paper "Surfacing the deep data of taxonomy" (based on a presentation I gave in 2011) has appeared in print as part to a special issue of

 Zookeys

: The manuscript was written shortly after the talk, but as is the nature of edited volumes it's taken a while to appear. My tweet about the paper sparked some interesting comments from David Shorthouse.

Surfacing the deep data of taxonomy

This post is a response to Ross Mounce's post Text mining for museum specimen identifiers. As Ross notes in that post, mining literature for specimen codes is something I've been interested in for a while (search for specimen codes on iPhylo), and @Aime Rankin (formerly an undergraduate student at Glasgow) did some work on this as well. It's great to see progress in this area.

Text mining for museum specimen identifiers

This a quick writeup of an analysis I did to make the case that the list of names held by the Index of Organism Names (ION) (part of Thomson Reuters) would be very useful for GBIF. I must declare a bias, in that I've spent a good chunk of the last 3-4 years exploring the ION database and investigating ways to link the taxonomic names it contains to the primary taxonomic literature, culminating in building BioNames.

The value of ION to GBIF

Playing with the my "material examined" tool I've been working on, I wondered whether I could make use of it in, say, a spreadsheet. Imagine that I have a spreadsheet of museum codes and want to look those up in GBIF. I could create a service for Open Refine but Open Refine is a bit big and clunky, you have to fire up a Java application and point your browser at it, and Open Refine isn't as intuitive or as flexible as a spreadsheet.

Looking up specimen codes in GBIF using Google Spreadsheet

Note to self for upcoming discussion with JournalMap.As of Monday August 25th, BioStor has 106,617 articles comprising 1,484,050 BHL pages. From the full text for these articles, I have extracted 45,452 distinct localities (i.e., geotagged with latitude and longitude). 15,860 BHL pages in BioStor pages have at least one geotag, these pages belong to 5,675 BioStor articles.In summary, BioStor has 5,675 full-text articles that are geotagged.

Geotagging stats for BioStor

This is guest post by Angelique Hjarding in response to discussion on this blog about the paper below.Thank you for highlighting our recent publication and for the very interesting comments. We wanted to take the opportunity to address some of the issues brought up in both your review and from reader comments. One of the most important issues that has been raised is the sharing of cleaned and vetted datasets.

Guest post: Response to the discussion on Red List assessments of East African chameleons

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).

Towards BioStor articles marked up using Journal Archiving Tag Set

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.

GBIF and open biodiversity data: what license should GBIF use?

In a previous post (Learning from eLife: GitHub as an article repository) I discussed the advantages of an Open Access journal putting its article XML in a version-controlled repository like GitHub. In response to that post Pensoft (the publisher of

 ZooKeys

) did exactly that, and the XML is available at https://github.com/pensoft/ZooKeys-xml.OK, "now what?" I hear you ask.

Augmenting ZooKeys bibliographic data to flesh out the citation graph

BioNames (http://bionames.org) is live. Getting to this point was supported by funding from EOL as part of their Computable Data Challenge. The award from EOL is paying for Ryan Schenk to work on the interface and overall design of the web site, and over the last few weeks we've been working increasingly frantically to get things ready. "Ready" is a relative concept.

BioNames now live  - Report on project

Came across this paper recently:Despite QR Codes being uncool, there's something appealing about the idea of compressing a DNA barcode sequence into a small image.

DNA QR Codes

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.

In defence of OpenURL: making bibliographic metadata hackable

Image by Mr.checker from Wikimedia Commons

 Science

carries a news piece on the perilous state of the International Commission on Zoological Nomenclature (on Twitter as @ZooNom):Pennisi, E. (2013). International Arbiter of Animal Names Faces Financial Woes. Science, 339(6122), 897–897.

The end of names? ICZN in financial crisis

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.

More GBIF specimen identifier strangeness

Following on from the SVG experiments I've started to put some of the Javascript code for displaying phylogenies on Github. Not a repository yet, but as gists, little snippets of code. Mike Bostock has created http://bl.ocks.org/ which makes it possible to host gists as working examples, so you can play with the code "live".The first gist takes a Newick tree, parses it and displays a tree.

NEXUS parser and tree viewer in Javascript

James Rosindell's OneZoom tree viewer is out and the paper describing the viewer has been published in PLoS One (disclosure, I was a reviewer):Below is a video where James describes OneZoom.OneZoom is fun, and is deservedly attracting a a lot of attention. But as visually striking as it is, I confess I have reservations about fractal-based viewers. For a start they make it hard to get a sense of the relative size of taxonomic groups.

OneZoom

For a current project I'm currently working I show organism distributions using data from GBIF, and I display that data on a map that uses the equirectangular projection.

Using orthographic projections to map organism distributions

Some quick notes on possibilities for text-mining BHL (in rough order of priority). Any text-mining would have to be robust to OCR errors.

BHL and text-mining: some ideas

Now we are awash in challenges! EOL has announced its Computable Data Challenge:Some $US 50,000 is on offer. "Challenge" is perhaps a misnomer, as EOL is offering this money not as a prize at the end, but rather to fund one or more proposals (submitted by 22 May) that are accepted.

EOL Computable Data Challenge community

Brief update on yesterday's post about finding specimens in BioStor. BioStor has some 66,000 articles from BHL, from which I've extracted 143,000 cases of a specimen code being cited in the text.

GBIF specimens in BioStor: who are the top ten museums with citable specimens?

Duplicate records are the bane of any project that aggregates data from multiple sources.

How many specimens does GBIF really have?

Quick note to self about exporting data from my Australian Faunal Directory on CouchDB project. To export data from a CouchDB view you can use a list function (see Formatting with Show and List). Following the example on the Kanapes IDE blog, I created the following list function: { "_id": "_design/publication", "_rev": "14-467dee8248e97d874f1141411f536848", "language": "javascript", "lists": { "tsv": "function(head,req) { var row;

Exporting data from Australian Faunal Directory on CouchDB

I've updated the BLAST a sequence and get a tree tool described in a previous post to output additional details, such as a list of the sequences used to build the tree and some basic metadata (such as the taxon name, name of any associated host, publication, and geographic coordinates). If the sequences are geotagged, then you will also see a little map showing the localities.

BLAST a sequence and get a tree and a map

Inspired by a comment on my post Visualising edit history of a Wikipedia page, the code I use to make history flow diagrams like the one below is now in GitHub at https://github.com/rdmpage/wikihistoryflow.There is also a live version at http://iphylo.org/~rpage/wikihistoryflow.

Wikipedia History Flow tool now in GitHub

How to cite:

 Page, R. (2011). Dark taxa: GenBank in a post-taxonomic world.

Dark taxa: GenBank in a post-taxonomic world

Charles Davies Sherborn, the Natural History Museum's 'magpie with a card-index mind’Next month I'll be speaking in London at The Natural History Museum at a one day event Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond.

Anchoring Biodiversity Information: from Sherborn to the 21st century and beyond

Quick post on a little tool I came across, moz-hocr-edit. This Firefox add-on lets you proofread Optical Character Recognition (OCR) output.

Correcting OCR using hOCR in Firefox

My paper describing the mapping between NCBI and Wikipedia has been published in PLoS Currents: Tree of Life. You can see the paper here. It's only just gone live, so it's yet to get a PubMed Central number (one of the nice features of PLoS Currents is that the articles get archived in PMC).Publishing in PLoS Currents: Tree of Life was a pleasant experience. The Google Knol editing environment was easy to use, and the reviewing process quick.

Paper on NCBI and Wikipedia published in PLoS Currents: Tree of Life

Déjà vu is a scary thing. Four years ago I released a mapping between names in TreeBASE and other databases called TBMap (described here: doi:10.1186/1471-2105-8-158). Today I find myself releasing yet another mapping, as part of my NCBI to Wikipedia project. By embedding the mapping in a wiki, it can be edited, so the kinds of problems I encountered with TbMap, recounted here, here, and here.

TreeBASE meets NCBI, again

Continuing experiments with a zoom viewer for large trees (see previous post), I've now made a demo where the labels are clickable. If the NCBI taxon has an equivalent page in Wikipedia the demo displays and link to that page (and, if present, a thumbnail image). Give it a try athttp://iphylo.org/~rpage/deeptree/3.htmlor watch the short video clip below: Zoomable viewer with Wikipedia thumbnails from Roderic Page on Vimeo.

Zooming a large tree, now with thumbnails

Quick note to express the frustration I experience sometimes when dealing with taxonomic literature.

Why metadata matters

Jeff Atwood, one of the co-founders of Stack Overflow recently wrote a blog post Trouble In the House of Google, where he noted that several sites that scrape Stack Overflow content (which Stack Overflow's CC-BY-SA license permits) appear

 higher in Google's search rankings than the original Stack Overflow pages

. When Stack Overflow chose the CC-BY-SA license they made the assumption that:Jeff Atwood's post goes on to argue that something

Why is the Atlas of Living Australia is invisible to Google?

Geoffery Bilder's comments about the unsuitability of URLs as long term identifiers (as opposed, say, to DOIs) came to mind when I discovered that the domain phthiraptera.org is up for sale: This domain used to be home to a wealth of resources on lice (order Phthiraptera). I discovered that ownership of the domain had expired when a bunch of links to PDFs returned by an iSpecies search for

 Collodennyus

all bounced to the holding page

The demise of phthiraptera.org and the perils of using Internet domain names as identifiers

One issue I'm running into with Mendeley is that it can create spurious documents, mangling my references in the process. This appears to be due to some over-zealous attempts to de-duplicate documents.

Mendeley mangles my references: phantom documents and the problem of duplicate references

Not really a blog post, more a note to self. If I ever did get around to writing a book again, I think

 
 Scripting Life
 

would be a great title.

Scripting Life

In previous articles I've looked at how various apps display scientific articles. The apps I looked at were:PLoS ReaderNaturePapersMendeleySo, where next? As Ian Mulvany noted in a comment on an earlier post, I haven't attempted to summarise the best user interface metaphors for navigation. Rather than try and do that in the abstract,  I'd like to create some prototypes to play with various ideas.

Viewing scientific articles on the iPad: browsing articles

Time (just) for a Friday folly. A couple of days ago the latest edition of the Catalogue of Life (CoL) arrived in my mailbox in the form of a DVD and booklet:While in some ways it's wonderful that the Catalogue of Life provides a complete data dump of its contents, this strikes me as a rather old-fashioned way to distribute it. So I began to wonder how this could be done differently, and started to think of CouchDB.

Replicating and forking data in 2010: Catalogue of Life and CouchDB

Dario Taraborelli has released ReaderMeter, an elegant app built on top of the Mendeley API. You enter an author's name and it summarises that authorship's readership in Mendeley.

ReaderMeter: what's in a name?

Apple's iBooks app is an ePub and PDF reader, and one could write a lengthy article about its interface. However, in the context of these posts on visualising the scientific article there's one feature that has particularly struck me. When reading a book that cited other literature the citations are hyper-links: click on one and iBooks forwards you (via the page turning effect) to the reference in the book's bibliography.

Viewing scientific articles on the iPad: iBooks

This week seems to be API week. The Encyclopedia of Life API Beta Test has been out since August 12th.

Navigating the Encyclopedia of Life tree on the desktop and the iPhone

Every so often I revisit the idea of browsing a collection of documents (or specimens, or phylogenies) geographically.

Browsing a digital library using a map

I've made some progress on a wiki of phylogenies. Still much to do, but here are some samples of what I'm trying to do.First up, here's an example of a publication http://iphylo.org/treebase/Doi:10.1016/j.ympev.2008.02.021:In addition to basic bibiographic details we have links to GenBank sequences and a phylogeny. The sequences are georeferenced, which enables us to generate a map.

Progress on a phylogeny wiki

I've written up some thoughts on Wikipedia for a short invited review to appear (pending review) in

 Organisms, Environment, and Diversity

(ISSN 1439-6092). The manuscript, entitled "Wikipedia as an encyclopaedia of life" is available as a preprint from Nature Precedings (hdl:10101/npre.2010.4242.1). The opening paragraph is:The content will be familiar to readers of this blog, although the essay is perhaps a slightly more sober assessment

Wikipedia manuscript

How to cite:

 Page, R. (2023). What, if anything, is the Biodiversity Knowledge Hub?

What, if anything, is the Biodiversity Knowledge Hub?

Lately I've become more and more interested in moving data off my machine(s) and into the cloud.

Zotero: creating bibliographies in the cloud

My delicious tags as a Wordle. In my defense I've not had nearly enough coffee today.

Displacement activity no. 37 - Wordle

I've updated my extension to resolve LSIDs in Firefox so that it works with version 1.5.0.1 (the most recent version of Firefox). The extension is available from Mozdev. It may take a little while for the mirrors to update with the new version, so if you get a "404" when trying to download, you may need to come back later. IBM's LSID project have their own Firefox extension LSID Launchpad for Firefox, which is a lot slicker than mine.

LSID Firefox extension update

I'm giving a short talk at the Workshop On Open Citations And Open Scholarly Metadata 2020, which will be held online on September 9th.

Workshop On Open Citations And Open Scholarly Metadata 2020 talk

The open access taxonomic journal ZooKeys has published a special issue with four papers, each available in HTML, PDF, and XML, the later being extensively marked up. Penev et al. ("Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples", doi:10.3897/zookeys.50.538) describes the process involved in creating these XML files.

ZooKeys publishes articles of the future

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.

BioNames one year on

Lucy Odling-Smee has a short piece on EoL in

 Nature

(doi:10.1038/news070508-7), quoting a certain Page chap as saying Not the most insightful thing I've ever said. One of the issues Lucy's piece highlights is the long term sustainability of electronic resources like EoL. The whole issue of digital curation is worrying, given the transient nature of many electronic resources.

More EoL commentary

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.

Displaying a million DNA barcodes on Google Maps using CouchDB

There's a slow-burning discussion on taxonomic concepts on Github that I am half participating in. As seems inevitable in any discussion of taxonomy, there's a lot of floundering about given that there's lots of jargon - much of it used in different ways by different people - and people are coming at the problem from different perspectives. In one sense, taxonomy is pretty straightforward.

Taxonomic publications as patch files and the notion of taxonomic concepts

A post by on the Plaza blog Expanded access to images in the Biodiversity Literature Repository has prompted me to write up a little toy I created earlier this week. The Biodiversity Literature Repository (BLR) is a repository of taxonomic papers hosted by Zenodo. Where possible Plazi have extracted individual images and added those to the BLR, even if the article itself is not open access.

Exploring images in the Biodiversity Literature Repository

Day three of TDWG 2017 highlighted some of the key obstacles facing biodiversity informatics. After a fun series of "wild ideas" (nobody will easily forget David Bloom's "Kill your Darwin Core darlings") we had a wonderful keynote by Javier de la Torre (@jatorre) entitled "Everything happens somewhere, multiple times". Javier is CEO and founder of Carto, which provides tools for amazing geographic visualisations.

TDWG 2017: thoughts on day 3

iPhylo

Roderic Page

For a short, but reasonably technical sumary of what I think the issues are, please read this "Technical Report", which I presented at the Workshop on Database Issues in Biological Databases (DBiBD) in Edinburgh in January 2005. This document is itself based on a BBSCR grant proposal which was funded. Here is the abstract.

iPhylo

Towards a Taxonomically Intelligent Phylogenetic Database

Introduction