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string: '{"archive_prefix":null,"backlog":0,"category":"computerAndInformationSciences","created_at":"2023-02-06","current_feed_url":null,"description":"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.","favicon":null,"feed_format":"application/atom+xml","feed_url":"https://iphylo.blogspot.com/feeds/posts/default","funding":null,"generator":"Blogger
7.00","home_page_url":"https://iphylo.blogspot.com","items":[{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/cgdvk-qhq18","id":"3749f8c4-1ba7-4e51-9dd6-9d9551ad451a","image":"https://lh3.googleusercontent.com/-nTpJfOuO7gI/VYqq2T3ERMI/AAAAAAAAD8I/AyWaatVuhjU/man03gTw_400x400.jpg?imgmax=800","indexed_at":1692828237,"language":"en","published_at":1435151040,"reference":[],"summary":"I
spent last Friday and Saturday at (Research in the 21st Century: Data,
Analytics and Impact, hashtag #ReCon_15) in Edinburgh. Friday 19th was
conference day, followed by a hackday at CodeBase. There''s a Storify archive
of the tweets so you can get a sense of the meeting. Sitting in the audience
a few things struck me. No identifier wars, DOIs have won and are everywhere.","tags":["DOI","GBIF","Github","ORCID"],"title":"Thoughts
on ReCon 15: DOIs, GitHub, ORCID, altmetric, and transitive credit","updated_at":1435154160,"url":"https://iphylo.blogspot.com/2015/06/thoughts-on-recon-15-dois-github-orcid.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/1exsv-82573","id":"c581f267-26fe-40c5-bb7c-a076592fe675","image":null,"indexed_at":1692831171,"language":"en","published_at":1421773740,"reference":[],"summary":"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 ma","tags":["Bitcoin","Ted
Nelson","Xanadu"],"title":"Bitcoin, Xanadu, Ted Nelson, and the web that wasn''t","updated_at":1421773807,"url":"https://iphylo.blogspot.com/2015/01/bitcoin-xanadu-ted-nelson-and-web-that.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/6v42p-x6315","id":"e7c43ce5-3f7d-4d3c-af11-5fe313852f1f","image":null,"indexed_at":1690499025,"language":"en","published_at":1534520880,"reference":[],"summary":"I''ve
made a video walkthrough of Ozymandias, which I described in this post. It''s
a bit, um, long, so I''ll need to come up with a shorter version. Ozymandias
- a biodiversity knowledge graph from Roderic Page on Vimeo.","tags":[],"title":"Ozymandias
demo","updated_at":1534520893,"url":"https://iphylo.blogspot.com/2018/08/ozymandias-demo.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/y6ajp-65548","id":"93d7ef76-44d8-4e8f-a89b-c983f6a496cd","image":null,"indexed_at":1693649746,"language":"en","published_at":1237397820,"reference":[],"summary":"Busy
day yesterday, giving two talks, one at The Natural History Museum, one at
the British Library. Slides for the NHM talk are below.","tags":["Biodiversity
Informatics","NHM","Talk","Taxonomy"],"title":"London Calling","updated_at":1237399513,"url":"https://iphylo.blogspot.com/2009/03/london-calling.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/x4sw2-rnm75","id":"c3f9992d-42f8-4180-a385-8c0227ae8daa","image":null,"indexed_at":1693650311,"language":"en","published_at":1235730060,"reference":[],"summary":"In
the wiki examples I''ve been developing I''ve been trying to model names using
the TDWG LSID vocabularies, particularly TaxonName. Roger Hyam has obviously
put a huge amount of work into developing these, and they handle just about
everything I need.","tags":["Chromis","Genus","LSID","Species","Taxonomy"],"title":"Something''s
missing from taxonomic name vocabularies","updated_at":1235731520,"url":"https://iphylo.blogspot.com/2009/02/somethings-missing-from-taxonomic-name.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/qvb47-c9598","id":"a18046cf-0d8f-478f-9041-594713fa5f34","image":"http://lh5.ggpht.com/-SaZvOanexaU/UjGQ6ncFMgI/AAAAAAAADBc/TPLLIVpVfAA/Gecko_Ptychozoon.intermedium.Malagos-copy-1.jpg?imgmax=800","indexed_at":1694116389,"language":"en","published_at":1378980060,"reference":[],"summary":"A
nice article by Brendan Borrell about the secret life of herpetologist Edward
Taylor, and Rafe Brown''s efforts to untangle his taxonomic legacy has appeared
in Nature:Borrell, B. (2013). Taxonomy: The spy who loved frogs. Nature,
501(7466), 150\u2013153. doi:10.1038/501150aFascinating article, but as always
I''m going to skip straight past the content and look at links.","tags":["Edward
Taylor","Links","Nature","Spy"],"title":"The spy who loved frogs and taxonomy
as a digital backwater","updated_at":1378980077,"url":"https://iphylo.blogspot.com/2013/09/the-spy-who-loved-frogs-and-taxonomy-as.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/xnmr6-yvw85","id":"2fc1020f-5572-4234-ba2c-e65426e070f9","image":"http://lh4.ggpht.com/-GuEIp2E_0Ns/T_6s1sVLk3I/AAAAAAAABh0/lr7VS0hnXoY/bob.jpg?imgmax=800","indexed_at":1692833599,"language":"en","published_at":1418112360,"reference":[],"summary":"The
following is a guest post by Bob Mesibov.","tags":["Bob Mesibov","Guest Post","Taxonomic
Name"],"title":"Guest post: Top 10 species names and what they mean","updated_at":1418114352,"url":"https://iphylo.blogspot.com/2014/12/guest-post-top-10-species-names-and.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/q7mg0-yq203","id":"1c3b90b7-5b71-4790-954d-41cc81ee5729","image":"https://lh3.googleusercontent.com/-f1Qp_gnxPKE/VYqfTwSJvnI/AAAAAAAAD7o/r4zX0O0IVps/Fig3-GoogleMaps-CC-BY-no-logo-300x205.png?imgmax=800","indexed_at":1692834189,"language":"en","published_at":1435148100,"reference":[],"summary":"I''ve
published a short note on my work on geophylogenies and GeoJSON in PLoS
Currents Tree of Life: Page R. Visualising Geophylogenies in Web Maps
Using GeoJSON. PLOS Currents Tree of Life. 2015 Jun 23 . Edition 1. doi:10.1371/currents.tol.8f3c6526c49b136b98ec28e00b570a1e.At
the time of writing the DOI hasn''t registered, so the direct link is here.
There is a GitHub repository for the manuscript and code.","tags":["Creative
Commons","Geo JSON","Geophylogeny","Github","P Lo S"],"title":"Visualising
Geophylogenies in Web Maps Using GeoJSON","updated_at":1435148196,"url":"https://iphylo.blogspot.com/2015/06/visualising-geophylogenies-in-web-maps.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/rnwpd-3nj27","id":"3088af1b-e520-484c-a19b-597b752e30af","image":null,"indexed_at":1692834792,"language":"en","published_at":1424436120,"reference":[],"summary":"Quick
notes on another example of data duplication in GBIF. I''m in the process
of building a tool to map specimen codes to GBIF records, and came across
the following example.","tags":["GBIF","OZCAM"],"title":"More examples of
data duplication and loss in GBIF: Australian bats in bits","updated_at":1424436298,"url":"https://iphylo.blogspot.com/2015/02/more-examples-of-data-duplication-and.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/2bpr6-11k45","id":"ef6ab647-fce3-438e-84c9-ac382e9b00b8","image":"http://lh3.googleusercontent.com/-Yd0pANREifI/VVSb1mQUpbI/AAAAAAAADvE/yM-vlri2Gas/ion-hdr-home.gif?imgmax=800","indexed_at":1692835932,"language":"en","published_at":1431608280,"reference":[],"summary":"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.","tags":["Bio Names","Birds","GBIF","Holotypes","ION"],"title":"The
value of ION to GBIF","updated_at":1431608428,"url":"https://iphylo.blogspot.com/2015/05/the-value-of-ion-to-gbif.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/ffpw6-tph57","id":"44a0fa62-2ece-4bb4-b02a-8fb80aa5a379","image":"http://lh6.ggpht.com/-ULRrbfCzLP4/UUBO4VIgHJI/AAAAAAAACg8/oNVBC5w5L3g/google.png?imgmax=800","indexed_at":1694177291,"language":"en","published_at":1363168980,"reference":[],"summary":"I
spend a lot of time searching the web for bibliographic metadata and links
to digitised versions of publications.","tags":["Google","Metadata","Pollution","Search"],"title":"Bibliographic
metadata pollution","updated_at":1363168997,"url":"https://iphylo.blogspot.com/2013/03/bibliographic-metadata-pollution.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/g6gq1-crg31","id":"aeb3d25e-03ca-414b-ae39-261743de0970","image":"http://lh4.ggpht.com/-DCo38jMQ49c/VS6LnOeVXGI/AAAAAAAADs4/ImzMGG8N1UI/material.png?imgmax=800","indexed_at":1692840645,"language":"en","published_at":1429113720,"reference":[],"summary":"I''ve
put together a working demo of some code I''ve been working on to discover
GBIF records that correspond to museum specimen codes. The live demo is at
http://bionames.org/~rpage/material-examined/ and code is on GitHub. To use
the demo, simply paste in a specimen code (e.g., \"MCZ 24351\") and click
Find and it will do it''s best to parse the code, then go off to GBIF
and see what it can find.","tags":["GBIF","Genbank","Knowledge Graph","Specimen
Codes"],"title":"Linking specimen codes to GBIF","updated_at":1429113761,"url":"https://iphylo.blogspot.com/2015/04/linking-specimen-codes-to-gbif.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/tpcn7-3tv55","id":"3b4f40b3-6c33-46af-9ec5-e60337c9509d","image":null,"indexed_at":1694042142,"language":"en","published_at":1416754680,"reference":[],"summary":"Quick
notes on an experimental feature I''ve added to BioNames. It attempts to identify
possible taxonomic synonyms by extracting pairs of names with the same species
name that appear together on the same page of text. The text could be full
text for an open access article, OCR text from BHL, or the title and abstract
for an article.","tags":["Bio Names","Data Mining","Synonyms"],"title":"Automatically
extracting possible taxonomic synonyms from the literature","updated_at":1416754725,"url":"https://iphylo.blogspot.com/2014/11/automatically-extracting-possible.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/bcgr8-8vr65","id":"c990a321-0b71-4734-aac2-444a18104aa2","image":"http://infosthetics.com/archives/manyeyes.jpg","indexed_at":1693653250,"language":"en","published_at":1171149600,"reference":[],"summary":"Spotted
on information aesthetics, IBM''s Many Eyes looks very cool. It''s a way to
share visualisations of data.","tags":[],"title":"Many Eyes","updated_at":1171149800,"url":"https://iphylo.blogspot.com/2007/02/many-eyes.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/q76g8-csq05","id":"56458587-f37a-4b45-b4f8-9916a0e41bf4","image":"http://lh3.ggpht.com/-exs6Ndm8dyA/VC0klVT0O3I/AAAAAAAADjc/Damjwy8Xrms/bj.png?imgmax=800","indexed_at":1694050300,"language":"en","published_at":1412244600,"reference":[],"summary":"Great
to see @JournalMap jump from ~11000 to ~17000 articles: http://t.co/bVarqDGGVU\u2014
Ken Mankoff (@mankoff) September 27, 2014The recent jump from ~11000 to ~17000
articles in JournalMap is mostly due to JournalMap ingesting content from
my BioStor database.","tags":["BHL","BHL Europe","Bio Stor","Journal Map"],"title":"BioStor
and JournalMap: a geographic interface to articles from the Biodiversity Heritage
Library","updated_at":1412244824,"url":"https://iphylo.blogspot.com/2014/10/biostor-and-journalmap-geographic.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/3y6rb-6cy61","id":"3f91cafd-a477-46fe-a4ce-ec4399cccb75","image":"http://lh3.ggpht.com/-WOBu1b7I8_Y/U4yAhv0Y4MI/AAAAAAAADWg/jbapI1083sI/b8e253dc3be3d84f2c69c51b0af86c03_400x400.png?imgmax=800","indexed_at":1694056551,"language":"en","published_at":1409227500,"reference":[],"summary":"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.","tags":["Bio Names","Cloudant","Couch
DB","Data"],"title":"BioNames database can be downloaded","updated_at":1409245723,"url":"https://iphylo.blogspot.com/2014/08/bionames-database-can-be-downloaded.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/any16-fw119","id":"2506fcee-d434-4618-8ebc-5214add6ce50","image":"http://lh5.ggpht.com/-IaI0Pb9t3yU/U_MU3KtZ7rI/AAAAAAAADgY/OCwLyZNK22M/AHjarding.JPG?imgmax=800","indexed_at":1694057028,"language":"en","published_at":1408439520,"reference":[],"summary":"This
is guest post by Angelique Hjarding in response to discussion on this blog
about the paper below.Hjarding, A., Tolley, K. A., & Burgess, N. D. (2014,
July 10). Red List assessments of East African chameleons: a case study of
why we need experts. Oryx. Cambridge University Press (CUP). doi:10.1017/s0030605313001427Thank
you for highlighting our recent publication and for the very interesting comments.","tags":["Chameleons","Data","Fig
Share","GBIF","Guest Post"],"title":"Guest post: Response to the discussion
on Red List assessments of East African chameleons","updated_at":1408440383,"url":"https://iphylo.blogspot.com/2014/08/guest-post-response-to-discussion-on.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/gr7hs-9bv39","id":"13ba98a3-19a4-4292-bcbc-099a1e6cf9cc","image":"http://a.tiles.mapbox.com/v3/timrobertson100.map-x2mlizjd/0/0/0.png","indexed_at":1694058769,"language":"en","published_at":1408038540,"reference":[],"summary":"Update:
Angelique Hjarding and her co-authors have responded in a guest post on
iPhylo.The quality and fitness for use of GBIF-mobilised data is a topic of
interest to anyone that uses GBIF data.","tags":["Chameleons","Data Quality","Expert","GBIF"],"title":"Seven
percent of GBIF data is usable - quick thoughts on Hjarding et al. 2014","updated_at":1408457813,"url":"https://iphylo.blogspot.com/2014/08/seven-percent-of-gbif-data-is-usable.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/998fg-fmt83","id":"020570e1-3f7b-4f6e-8ad6-6fd05276f203","image":"http://lh5.ggpht.com/-pV2hYzzsZE0/Ug0KZCrTppI/AAAAAAAAC-w/xIPh-lGP9cQ/birds.png?imgmax=800","indexed_at":1694119981,"language":"en","published_at":1376586300,"reference":[],"summary":"One
feature I''ve always wanted to have in BioNames is a timeline of taxonomic
names. ION has one (see here), but I wanted a way to go from the timeline
to the actual publications.","tags":["Bio Names","Taxonomy","Timeline"],"title":"BioNames
update - taxonomic name timelines","updated_at":1376586355,"url":"https://iphylo.blogspot.com/2013/08/bionames-update-taxonomic-name-timelines.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/dq1cv-szd96","id":"2a9c8af6-e022-4165-8d2d-761ec6b43917","image":"http://lh4.ggpht.com/-yX2f7U5J3Ew/UguXr3UxOaI/AAAAAAAAC-Q/3_TiV9T8GaM/bats.png?imgmax=800","indexed_at":1694121331,"language":"en","published_at":1376491440,"reference":[],"summary":"Continuing
the theme of the failings of the GBIF classification I''ve been playing further
with cluster maps to visualise the problem (see this earlier post for an introduction).Browsing
through bats in GBIF I keep finding the same species appearing more than once,
albeit in different genera.","tags":["Bats","Classification","Cluster Maps","Data
Cleaning","GBIF"],"title":"Cluster maps, papaya plots, and the trouble with
GBIF taxonomy","updated_at":1376491534,"url":"https://iphylo.blogspot.com/2013/08/cluster-maps-papaya-plots-and-trouble.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/ch96r-vgg12","id":"b709e402-6ab8-4549-872b-d9bf37bc97f3","image":"http://www.w3.org/RDF/icons/rdf_w3c_icon.128","indexed_at":1694122391,"language":"en","published_at":1375356120,"reference":[],"summary":"Readers
of this blog will know that I''m sceptical about the current value of linked
data and RDF in biodiversity informatics. But I came across an interesting
paper on RDF and biocuration that suggests a good \"use case\" for RDF in
constructing and curating taxonomic databases.The paper is \"Catching inconsistencies
with the semantic web: a biocuration case study\" (PDF here) by Jerven Bolleman
and Sebastien Gehant.","tags":["Data Cleaning","RDF","SPARQL","Taxonomy","Uniprot"],"title":"A
use case for RDF in taxonomy","updated_at":1375959052,"url":"https://iphylo.blogspot.com/2013/08/a-use-case-for-rdf-in-taxonomy.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/dy88v-k2h60","id":"0d0ab57c-8a1b-48bc-938f-2fb6836756fe","image":"http://lh4.ggpht.com/_Gct8lVAxKqQ/S2MLTZsXFvI/AAAAAAAAAmU/ayovV3f-nDc/best_experience_20100127.png?imgmax=800","indexed_at":1693656264,"language":"en","published_at":1264785240,"reference":[],"summary":"OK,
first of all, I want one, I want one real bad.There''s been a general sense
of disappointment about the iPad, which I suspect is only natural given the
enormous hype leading up to the announcement, as well as the fact that the
applications shown were fairly conventional.","tags":["Apple","I Pad","Perceptive
Pixel","Touch Screen"],"title":"Why I want an iPad","updated_at":1264845717,"url":"https://iphylo.blogspot.com/2010/01/why-i-want-ipad.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/26ame-4a164","id":"cd532f4b-02b6-400d-98b6-283949613f02","image":null,"indexed_at":1693657056,"language":"en","published_at":1256289300,"reference":[],"summary":"Continuing
with my exploration of the Biodiversity Heritage Library one obstacle to linking
BHL content with nomenclature databases is the lack of a consistent way to
refer to the same bibliographic item (e.g., book or journal). For example,
the Amphibia Species of the World (ASW) page for Gastrotheca aureomaculata
gives the first reference for this name as: Gastrotheca aureomaculata Cochran
and Goin, 1970, Bull. U.S. Natl.","tags":["BHL","Data Cleaning","Index","Matching","My
SQL"],"title":"n-gram fulltext indexing in MySQL","updated_at":1256293788,"url":"https://iphylo.blogspot.com/2009/10/n-gram-fulltext-indexing-in-mysql.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/w8gf3-ggq95","id":"fc15de58-c7ef-4044-8195-3b55d4b6bdbf","image":null,"indexed_at":1693657918,"language":"en","published_at":1229413980,"reference":[],"summary":"I''m
in the US on UK time, so this is probably a bad idea to write this, but the
paper by Malte Ebach et al. (\"O Cladistics, Where Art Thou?\", doi:10.1111/j.1096-0031.2008.00225.x)
in the latest Cladistics just annoys me too much.","tags":["Cladistics","Ideology","Rant"],"title":"Death
throes of Cladistics","updated_at":1229419355,"url":"https://iphylo.blogspot.com/2008/12/death-throes-of-cladistics.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/52qwe-6yh44","id":"6dbada82-a50f-4439-9f45-a0fd6e9bd8cf","image":"https://lh3.googleusercontent.com/-1XZ61dPP9RU/V7SXvuFJO5I/AAAAAAAAEP8/FDrRi3cmHDs/docker.png?imgmax=1600","indexed_at":1690411979,"language":"en","published_at":1471453140,"reference":[],"summary":"Some
notes on containers, microservices, and data. The idea of packaging software
into portable containers and running them either locally or in the cloud is
very attractive (see Docker). Some use cases I''m interested in exploring.","tags":["Containers","Docker","Microservices"],"title":"Containers,
microservices, and data","updated_at":1471453144,"url":"https://iphylo.blogspot.com/2016/08/containers-microservices-and-data.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/9tafr-k2g51","id":"eaf4ab1a-2953-462f-bd6c-0167ae8dad48","image":"https://lh3.googleusercontent.com/-BjF-Bq67ygc/WEk4NGxNZcI/AAAAAAAAEVM/h1gYX6PM_rU/Screenshot%2525202016-12-07%25252022.58.43.png?imgmax=1600","indexed_at":1690411365,"language":"en","published_at":1481193480,"reference":[],"summary":"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.","tags":["DNA Barcoding","GBIF","I BOL"],"title":"iBOL DNA barcodes
in GBIF","updated_at":1481193730,"url":"https://iphylo.blogspot.com/2016/12/ibol-dna-barcodes-in-gbif.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/z4akv-d5d52","id":"2ac0ba77-fc71-4027-9d91-0b5130529609","image":"http://lh6.ggpht.com/-p6BlPDVHDmw/UPUpIYqbgPI/AAAAAAAACYQ/OUFwgIcW6tM/logo.png?imgmax=800","indexed_at":1694191992,"language":"en","published_at":1358244120,"reference":[],"summary":"The
Integrated Digitized Biocollections (iDigBio) project aims to advance digitising
US biodiversity collections. They recently published a GUID Guide for Data
Providers.","tags":["Identifiers","I Dig Bio","Linking","Specimens","USNM"],"title":"iDigBio:
You are putting identifiers on the wrong thing","updated_at":1358254720,"url":"https://iphylo.blogspot.com/2013/01/idigbio-you-are-putting-identifiers-on.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/zm95w-jhf98","id":"4734b7dc-b036-4630-ad0e-cc8ee5e70c53","image":null,"indexed_at":1693659825,"language":"en","published_at":1239177120,"reference":[],"summary":"The
e-Biosphere online forum has a topic entitled Why open source code? Why not
patented softwares?. This thread was started by Mauri \u00c5hlberg, who notes
that the EOL codebase is open source, and asks \"why not patent software.\"
\u00c5hlberg has patented NatureGate (US Patent 7400295), which claims:In
the method of the invention objects can be identified on the basis of location
and one or more characteristics in an improved way.","tags":["E Biosphere","Patent"],"title":"Patenting
biodiversity tools","updated_at":1239202887,"url":"https://iphylo.blogspot.com/2009/04/patenting-biodiversity-tools.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/3yz8k-sxx07","id":"a8891a05-8201-482c-a318-08ba39c2ebdd","image":"https://lh3.googleusercontent.com/-n_eSRAFqBR4/VzK7mPDxiOI/AAAAAAAAENQ/AZBl5X3L1Mc/images.png?imgmax=1600","indexed_at":1690414377,"language":"en","published_at":1462942560,"reference":[],"summary":"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.","tags":["NCBI","Scott Federhen"],"title":"Scott
Federhen","updated_at":1462942748,"url":"https://iphylo.blogspot.com/2016/05/scott-federhen-rip.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/s2q13-6v062","id":"746c116a-ef49-490d-b4e5-58e8541c05c1","image":"https://lh3.googleusercontent.com/-uE577wBJnew/WvMd0RH2doI/AAAAAAAAEo8/IwovHJPFwrYkz4DEBSyT2i-Wcj24XcQTwCHMYCw/s0/Screenshot+2018-05-09+16.58.00.png","indexed_at":1690495450,"language":"en","published_at":1525882320,"reference":[],"summary":"It''s
been a little quiet on this blog as I''ve been teaching, and spending a lot
of time data wrangling and trying to get my head around \"data lakes\" and
\"triple stores\". So there are a few things to catch up on, and a few side
projects to report on. I continue to play with iSpecies, which is a simple
mashup off biodiversity data sources.","tags":["I Species"],"title":"iSpecies
meets Lifemap","updated_at":1525886810,"url":"https://iphylo.blogspot.com/2018/05/ispecies-meets-lifemap.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/2wypt-xap34","id":"8cc789d3-ce7d-4d5f-ac8a-2c3ca5a145c1","image":"http://lh6.ggpht.com/_Gct8lVAxKqQ/SyKGilzF-nI/AAAAAAAAAk8/DtsQfWAgpPE/46740423.png?imgmax=800","indexed_at":1693660552,"language":"en","published_at":1260555600,"reference":[],"summary":"I''ve
been buried in programming (and it''s exam time at Glasgow) so I''ve not blogged
for a month (gasp). I''ve been playing with ways to visualise Biodiversity
Heritage Library content for a while (click here for a list of previous posts),
and have occasionally surfaced to tweet a screenshot via twitpic.","tags":["BHL","Twitter","Visualisation"],"title":"BHL
interface ideas","updated_at":1260555625,"url":"https://iphylo.blogspot.com/2009/12/bhl-interface-ideas.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/xwpw0-p8t97","id":"c107fe91-d86c-42ba-844b-981103a54843","image":"https://lh3.googleusercontent.com/-N8HwX4pcmHc/WgWOPB0CRkI/AAAAAAAAEjc/BV2hYcCggZ0iZSnjk6mQgvDrc1P1zrmVgCHMYCw/Screenshot%2B2017-11-10%2B11.03.30.png?imgmax=1600","indexed_at":1690504054,"language":"en","published_at":1510313520,"reference":[],"summary":"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.","tags":["BHL","BLR","Copyright","Images","Zenodo"],"title":"Exploring
images in the Biodiversity Literature Repository","updated_at":1510313559,"url":"https://iphylo.blogspot.com/2017/11/exploring-images-in-biodiversity.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/k5syz-mpb09","id":"8cea8fe1-d99d-4bb8-adae-128db5ae7fda","image":null,"indexed_at":1690503198,"language":"en","published_at":1507296840,"reference":[],"summary":"Notes
on how many georeferenced DNA sequences there are in GenBank, and how many
could potentially be georeferenced.","tags":["GBIF","Genbank","Georeferencing","Note
To Self"],"title":"Notes on finding georeferenced sequences in GenBank","updated_at":1507296869,"url":"https://iphylo.blogspot.com/2017/10/notes-on-finding-georeferenced.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/e6xt3-qgz08","id":"a3a5c6ef-4e33-44d0-a02f-c96dc7e058b9","image":"https://lh3.googleusercontent.com/-bSZ2rtl5XK0/WvMu-R7ZgZI/AAAAAAAAEpc/omPFYuhNh5sTBND4dAbH_rRvTbljopoUQCHMYCw/s0/http---images.ctfassets.net-uo17ejk9rkwj-L6lRFOvdQG4M4yY0k0Cei-ad53f85a57368b017fecb8907393d32a-ebbe-2018.png","indexed_at":1690501975,"language":"en","published_at":1525886700,"reference":[],"summary":"Last
year I finished my four-year stint as Chair of the GBIF Science Committee.
During that time, partly as a result of my urging, GBIF launched an annual
\"GBIF Ebbe Nielsen Challenge\", and I''m please that this year GBIF is continuing
to run the challenge. In 2015 and 2016 the challenge received some great entries.","tags":["Challenge","GBIF"],"title":"2018
GBIF Ebbe Nielsen Challenge now open","updated_at":1525886782,"url":"https://iphylo.blogspot.com/2018/05/2018-gbif-ebbe-nielsen-challenge-now.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/3qkvr-h8657","id":"217a651d-b4ae-452c-aa79-f9deb95dbe19","image":"https://lh3.googleusercontent.com/-WTKsjoezA4Y/VmgvGcC3MpI/AAAAAAAAEFg/wi3v6Y7qjmU/treediff.png?imgmax=800","indexed_at":1692999194,"language":"en","published_at":1449668340,"reference":[],"summary":"It''s
a nice feeling when work that one did ages ago seems relevant again. Markus
D\u00f6ring has been working on a new backbone classification of all the species
which occur in taxonomic checklists harvested by GBIF. After building a new
classification the obvious question arises \"how does this compare to the
previous GBIF classification?\" A simple question, answering it however is
a little tricky.","tags":["Algorithm","Difference","GBIF","Github","Tree Edit"],"title":"Visualising
the difference between two taxonomic classifications","updated_at":1449668381,"url":"https://iphylo.blogspot.com/2015/12/visualising-difference-between-two.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/2ntg3-gsh56","id":"4b88ca40-e0fd-446c-a4f2-6e5e144089d5","image":"https://lh3.googleusercontent.com/-9UV9V0DR-0s/WKTYLK_TwlI/AAAAAAAAEYU/dES4Jb10ToM/Screenshot%2525202017-02-15%25252019.28.17.png?imgmax=1600","indexed_at":1690408375,"language":"en","published_at":1487198280,"reference":[],"summary":"At
present BioStor provides a simple display of an article extracted from BHL.
You get the page images, and sometimes a map and an altmetric \"donut\". But
we can do better than this. For example, I''m starting to experiment with
displaying a list of literature cited by the article.","tags":["Bio Stor","Citations","Pub
Med"],"title":"New feature for BioStor: extracting literature cited from OCR
text","updated_at":1487198304,"url":"https://iphylo.blogspot.com/2017/02/new-feature-for-biostor-extracting.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/tndg4-0x949","id":"122ca6be-81f4-43fb-b769-9924f3fc2ec5","image":"http://upload.wikimedia.org/wikipedia/commons/thumb/e/e0/Wikispecies-logo.jpg/511px-Wikispecies-logo.jpg","indexed_at":1693662182,"language":"en","published_at":1249628460,"reference":[],"summary":"This
post was prompted by Stephen Thorpe''s post on TAXACOM about Wikispecies in
which he wrote (in a thread discussing Roger Hyam''s recent blog post) that[i]f
it [Wikispecies] isn''t a true database, then it is BETTER than a database.
It can do anything a database can do, and more, if you know how it works
properly.I beg to differ.","tags":["Database","Wikispecies"],"title":"Wikispecies
is not a database","updated_at":1249630055,"url":"https://iphylo.blogspot.com/2009/08/wikispecies-is-not-database.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/wnhjf-9c704","id":"21004334-9958-4687-a084-5b8c1c3a548f","image":"http://lh5.ggpht.com/_Gct8lVAxKqQ/Spfyk-Q-2bI/AAAAAAAAAhI/M4Hn2OwtOF8/m.jpg?imgmax=800","indexed_at":1693661581,"language":"en","published_at":1251473280,"reference":[],"summary":"As
part of my on-going experiments with Wikipedia as a repository of taxonomic
information, I''ve extracted mammal pages from Wikipedia.","tags":[],"title":"Visualising
the Wikipedia classification of mammals","updated_at":1251529448,"url":"https://iphylo.blogspot.com/2009/08/visualising-wikipedia-classification-of.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/97a6s-ymc08","id":"61e720ec-aae4-41b3-97cb-eef187e5b9dc","image":"https://lh3.googleusercontent.com/-IGEq8nV1tkI/V7WzH7QWSPI/AAAAAAAAEQM/Kiqf7quGp8I/Screenshot%2525202016-08-18%25252014.04.03.png?imgmax=1600","indexed_at":1690422778,"language":"en","published_at":1471525620,"reference":[],"summary":"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.","tags":["Bio Stor","Leaflet","Open
Refine","Stamen"],"title":"BioStor updates: nicer map, reference matching
service","updated_at":1471525666,"url":"https://iphylo.blogspot.com/2016/08/biostor-updates-nicer-map-reference.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/gp59b-1hr51","id":"ceb9b2b0-aee1-466d-a90f-65306e47f0a8","image":null,"indexed_at":1690511593,"language":"en","published_at":1503225840,"reference":[],"summary":"Notes
to self on web map-style tree viewers. The basic idea is to use Google Maps
or Leaflet to display a tree. Hence we need to compute tiles. One approach
is to use a database that supports spatial queries to store the x,y coordinates
of the tree.","tags":["Google Maps","Javascript","Leaflet","Note To Self","Phylogeny"],"title":"Notes
on displaying big trees using Google Maps/Leaflet","updated_at":1503225889,"url":"https://iphylo.blogspot.com/2017/08/notes-on-displaying-big-trees-using.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/z0aqm-v6389","id":"64803e56-d4b1-425e-8daf-2f1b0206cdff","image":"https://lh3.googleusercontent.com/-1t4CZaAYVmE/WS69736rwEI/AAAAAAAAEcM/T1GL-Hx58hIyiYK_rXhApET5ox6YdlEhwCHM/Screenshot%2B2017-05-31%2B12.46.43.png?imgmax=1600","indexed_at":1690512770,"language":"en","published_at":1496235960,"reference":[],"summary":"Last
week I was at WikiCite 2017, a fascinating three day event in Vienna. Wikicite
is \"a proposal to build a bibliographic database in Wikidata to serve all
Wikimedia projects\", and is attracting increasing attention from academics,
librarians, publishers, data geeks, and others. You can get a sense of the
project by following @WikiCite on Twitter.","tags":["BHL","Crossref","Gene
Wiki","WikiCite","Wikidata"],"title":"Wikidata, WikiCite, and the \"bibliography
of life\"","updated_at":1496235994,"url":"https://iphylo.blogspot.com/2017/05/wikidata-wikicite-and-of-life.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/88p92-7kz89","id":"0c439b23-1618-44b1-b3e6-8e2d753833c6","image":null,"indexed_at":1690514141,"language":"en","published_at":1496240220,"reference":[],"summary":"Over
7 million #SPARQL queries/day in @wikidata #WikiCite \ud83d\udc4f\ud83c\udffb
pic.twitter.com/l2I6IcnGJj\u2014 WikiCite (@Wikicite) May 23, 2017 For my
own use more than anything else I''ve started creating a list of Wikidata
SPARQL queries here. I personally don''t find Wikidata''s data model particularly
easy to grasp, so one way to learn is to take the example queries on the Wikidata
Query site and mess about with them.","tags":["SPARQL","Wikidata"],"title":"Querying
Wikidata","updated_at":1496240230,"url":"https://iphylo.blogspot.com/2017/05/querying-wikidata_31.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/2pkth-pf821","id":"66d8edc9-9439-45a3-aa9d-98479aa59b68","image":"http://lh5.ggpht.com/-GJNdblTTm40/UMHWjodZu_I/AAAAAAAACUs/mYA7EytAQAs/sampleimg2.png?imgmax=800","indexed_at":1694200474,"language":"en","published_at":1354880640,"reference":[],"summary":"Say
what you will about Elsevier, they are certainly exploring ways to re-imagine
the scientific article. In a comment on an earlier post Fabian Schreiber pointed
out that Elsevier have released an app to display phylogenies in articles
they publish. The app is based on jsPhyloSVGand is described here.","tags":["Article
2 0","Elsevier","Javascript","Phylogeny","SVG"],"title":"Elsevier articles
have interactive phylogenies","updated_at":1354880669,"url":"https://iphylo.blogspot.com/2012/12/elsevier-articles-have-interactive.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/p0zrm-f5494","id":"b510a8e5-7f5c-42af-9e9e-209db89c2bc2","image":"https://lh3.googleusercontent.com/-Ls16PL3dXM4/V7XILtOiAHI/AAAAAAAAEQc/PnE77JlmAy4/Screenshot%2525202016-08-18%25252015.13.59.png?imgmax=1600","indexed_at":1690413314,"language":"en","published_at":1471531080,"reference":[],"summary":"In
a classic paper Boggs (1949) appealed for an \u201catlas of ignorance\u201d,
an honest assessment of what we know we don\u2019t know: Boggs, S. W.. (1949).
An Atlas of Ignorance: A Needed Stimulus to Honest Thinking and Hard Work.
Proceedings of the American Philosophical Society, 93(3), 253\u2013258.","tags":["Challenge","Gaps","GBIF","Hurlberts
Index","OBIS"],"title":"GBIF Challenge: \u20ac31,000 in prizes for analysing
and addressing gaps and biases in primary biodiversity data","updated_at":1471531085,"url":"https://iphylo.blogspot.com/2016/08/gbif-challenge-31000-in-prizes-for.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/8jtg0-vtg66","id":"b2440ee0-8550-48e8-91e5-b12ec0b98697","image":"https://lh3.googleusercontent.com/-GqDD5iZJqXY/WDa8gDzG7fI/AAAAAAAAEUc/sScQQbFOrIg/Screenshot%2525202016-11-24%25252010.08.22.png?imgmax=1600","indexed_at":1690424039,"language":"en","published_at":1479981960,"reference":[],"summary":"Continuing
my on-again off-again relationship with the Semantic Web, I stumbled across
a cool approach to visualising the results of SPARQL queries.","tags":["D
3","Javascript","Semantic Web","SPARQL","Visualisation"],"title":"The Semantic
Web made fun: d3sparql","updated_at":1481555465,"url":"https://iphylo.blogspot.com/2016/11/the-semantic-web-made-fun-d3sparql.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/9dj95-jqg69","id":"46ba738d-ba33-4d01-96bb-e4faa6bc8635","image":null,"indexed_at":1690426370,"language":"en","published_at":1470828660,"reference":[],"summary":"In
between complaining about the lack of open data in biodiversity (especially
taxonomy), and scraping data from various web sites to build stuff I''m interested
in, I occasionally end up having interesting conversations with the people
whose data I''ve been scraping, cleaning, cross-linking, and otherwise messing
with. Yesterday I had one of those conversations at Kew Gardens.","tags":["Defra","Kew","Open
Data"],"title":"On asking for access to data","updated_at":1470828713,"url":"https://iphylo.blogspot.com/2016/08/on-asking-for-access-to-data.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/h6xee-ma520","id":"a277085d-e813-4f18-b53b-3a788c8bfab9","image":"http://lh4.ggpht.com/-_yW2vvON4PA/UKyXmjLZCDI/AAAAAAAACQA/ZbG9SkRpmns/21.png?imgmax=800","indexed_at":1694208798,"language":"en","published_at":1353488280,"reference":[],"summary":"Benoi\u0302t
Fontaine et al. recently published a study concluding that average lag time
between a species being discovered and subsequently described is 21 years.Fontaine,
B., Perrard, A., & Bouchet, P. (2012). 21 years of shelf life between discovery
and description of new species. Current Biology, 22(22), R943\u2013R944.","tags":["Biodiversity","Data","Taxonomy"],"title":"Species
wait 21 years to be described - show me the data","updated_at":1353488291,"url":"https://iphylo.blogspot.com/2012/11/species-wait-21-years-to-be-described.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/99cvt-94e65","id":"3686a0f3-b480-489a-84dc-30ee2ffc4007","image":"https://lh3.googleusercontent.com/-p1lzN04RdZg/WHoQzuBIeRI/AAAAAAAAEXI/1_gTWxnZ4vo/Screenshot%2525202017-01-14%25252011.41.55.png?imgmax=1600","indexed_at":1690413773,"language":"en","published_at":1484394660,"reference":[],"summary":"Following
on from previous posts The Semantic Web made fun: d3sparql and The Biodiversity
Heritage Library meets Wikidata via Wikispecies: adding author identifiers
to BioStor I''ve put together an example query that can be used to extract
a taxonomic classification from Wikidata.","tags":["Classification","D 3 Js","RDF","SPARQL","Wikidata"],"title":"Displaying
taxonomic classifications from Wikidata using d3js and SPARQL","updated_at":1484394868,"url":"https://iphylo.blogspot.com/2017/01/displaying-taxonomic-classifications.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/536f4-zt966","id":"dbf56f4c-5e89-4266-9364-3ea7935f4949","image":null,"indexed_at":1690505366,"language":"en","published_at":1490364720,"reference":[{"key":"ref1","url":"https://ncbi.nlm.nih.gov/pmc/articles/pmc2674678"},{"doi":"https://doi.org/10.1186/1471-2105-10-s14-s4","key":"ref2"},{"doi":"https://doi.org/10.1186/1471-2105-10-s14-s9","key":"ref3"},{"doi":"https://doi.org/10.1126/science.aaf4381","key":"ref4"},{"doi":"https://doi.org/10.1093/nar/gkn075","key":"ref5"}],"summary":"Following
on from earlier posts exploring how to map DNA barcodes and putting barcodes
into GBIF it''s time to think about taking advantage of what makes barcodes
different from typical occurrence data. At present GBIF displays data as dots
on a map (as do I in http://iphylo.org/~rpage/bold-map/). But barcodes come
with a lot more information than that.","tags":["Alignment Free Phylogeny","DNA
Barcoding","ElasticSearch","GGBN","Phylogenetic Diversity"],"title":"This
is what phylodiversity looks like","updated_at":1490364753,"url":"https://iphylo.blogspot.com/2017/03/this-is-what-phylodiversity-looks-like.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/y5xy3-f0h42","id":"af20e30d-91ee-4855-8580-1370555272e2","image":null,"indexed_at":1690428208,"language":"en","published_at":1464269280,"reference":[],"summary":"Given
that Wikipedia, Wikidata, and the Biodiversity Heritage Library (BHL) all
share the goal of making information free, open, and accessible, there seems
to be a lot of potential for useful collaboration. Below I sketch out some
ideas. BHL as a source of references for Wikipedia Wikipedia
likes to have sources cited to support claims in its articles. BHL has a lot
of articles that could be cited by Wikipedia articles.","tags":["BHL","Wikidata","Wikipedia"],"title":"Thoughts
on Wikipedia, Wikidata, and the Biodiversity Heritage Library","updated_at":1464269333,"url":"https://iphylo.blogspot.com/2016/05/thoughts-on-wikipedia-wikidata-and.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/b1v0e-7k456","id":"41061221-46ba-4399-a5b6-40894f7cfbbc","image":"https://lh3.googleusercontent.com/-Osd6Nj0BFeg/VucEv6goavI/AAAAAAAAEI0/GGkNKQ9vNsg/fig-1-full.png?imgmax=800","indexed_at":1692996175,"language":"en","published_at":1457980560,"reference":[],"summary":"TL;DR;
In order to build a usable biodiversity knowledge graph we should adopt JSON-LD
for biodiversity data, develop reconciliation services to match entities to
identifiers, and a use a mixture of document and graph databases to store
and query the data. To bootstrap this project we can create wrappers around
each biodiversity data provider, and a central cache that is both a document
store and a simple graph database.","tags":["Knowledge Graph"],"title":"Towards
a biodiversity knowledge graph","updated_at":1457980610,"url":"https://iphylo.blogspot.com/2016/03/towards-biodiversity-knowledge-graph.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/sr14e-msk39","id":"69b0ff9d-1491-4053-9a8a-30445712af40","image":"http://lh5.ggpht.com/-QxYtoPfhumM/UIVLi5sE2QI/AAAAAAAACKw/tK4yyS9cfn0/cms-logo.png?imgmax=800","indexed_at":1694214247,"language":"en","published_at":1350912900,"reference":[],"summary":"We
don''t need no stinkin'' parser- a guide to resolving free-form citations
with #CrossRef Metadata Search -> goo.gl/f9a4e\u2014 Geoffrey Bilder (@gbilder)
October 18, 2012CrossRef have released CrossRef Metadata Search a nice tool
that can take a free-form citation and return possible matches from CrossRef''s
database.","tags":["Citation Matching","Cloudant","Couch DB","Crossref"],"title":"Resolving
free-form citations","updated_at":1350912912,"url":"https://iphylo.blogspot.com/2012/10/resolving-free-form-citations.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/asxj6-zb876","id":"6f47ac3d-88ce-4336-8b9d-85edd197b041","image":null,"indexed_at":1690425905,"language":"en","published_at":1471014720,"reference":[],"summary":"I''ve
been experimenting with simple spatial search in BioStor, as shown in the
demo below. If you go to the map on BioStor you can use the tools on the left
to draw a box or a polygon on the map, and BioStor will search it''s database
for articles that mention localities that occur in that region. If you click
on a marker you can see the title of the article, clicking on that title takes
you to the article itself.","tags":["BHL","Bio Stor","Cloudant","Couch DB"],"title":"Spatial
search in BioStor","updated_at":1471014745,"url":"https://iphylo.blogspot.com/2016/08/spatial-search-in-biostor.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/gf1dw-n1v47","id":"a41163e0-9c9a-41e0-a141-f772663f2f32","image":"https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZweukxntl7R5jnk3knVFVrqZ5RxC7mPZBV4gKeDIglbFzs2O442nbxqs8t8jV2tLqCU24K6gS32jW-Pe8q3O_5JR1Ms3qW1aQAZ877cKkFfcUydqUba9HsgNlX-zS9Ne92eLxRGS8F-lStTecJw2oalp3u58Yoc0oM7CUin5LKPeFIJ7Rzg/s400/_DSC5106.jpg","indexed_at":1689959133,"language":"en","published_at":1678762800,"reference":[],"summary":"My
dad died last weekend. Below is a notice in today''s New Zealand Herald. I''m
in New Zealand for his funeral. Don''t really have the words for this right
now.","tags":[],"title":"Dugald Stuart Page 1936-2022","updated_at":1679469956,"url":"https://iphylo.blogspot.com/2023/03/dugald-stuart-page-1936-2022.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/y5nzb-w3z09","id":"f7459694-a392-4ddb-8bdb-404f7aa81df9","image":"http://lh3.ggpht.com/-FnGUhB6epKc/UIEyj98KHII/AAAAAAAACJ4/zONddb03tts/6892585935_32d4e21e77_o.png?imgmax=800","indexed_at":1694214934,"language":"en","published_at":1350644340,"reference":[],"summary":"Only
4% of all published phylogenies have data in #treebase or @datadryad\u2014
Karen Cranston (@kcranstn) October 18, 2012It is well known that phylogeny
databases such as TreeBASE capture a small fraction of the published phylogenies.
This raises the question of how to increase the number of trees that get archived.","tags":["Database","Phylogeny","Phy
Lo TA","Piracy","Sociology"],"title":"The failure of phylogeny databases","updated_at":1350646920,"url":"https://iphylo.blogspot.com/2012/10/the-failure-of-phylogeny-databases.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/yh7cw-shy15","id":"ed40c989-0ce6-4e0d-a1e9-7152a9e90986","image":null,"indexed_at":1693667043,"language":"en","published_at":1229163960,"reference":[],"summary":"The
latest post on the EOL blog (Biodiversity in a rapidly changing world) really,
really annoys me. It claims thatThe case of the red lionfish exemplfies how
EOL can provide information for science-based decision making. Red lionfish
are native to coral reef ecosystems in the Indo-Pacific.","tags":["EOL","GBIF","I
Species","Red Lionfish","Sucks"],"title":"EOL hyperbole","updated_at":1229181686,"url":"https://iphylo.blogspot.com/2008/12/eol-hyperbole.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/t4kch-dhq91","id":"b2d8664e-f2b0-479b-afed-77df1d2af353","image":null,"indexed_at":1693667730,"language":"en","published_at":1229676300,"reference":[],"summary":"Test
of google-code-prettify:class Voila {public: // Voila static const string
VOILA = \"Voila\"; // will not interfere with embedded tags.}","tags":[],"title":"Code
prettyfier","updated_at":1230643897,"url":"https://iphylo.blogspot.com/2008/12/code-prettyfier.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/m33gh-adh33","id":"ac27e696-7bba-4600-a5e6-c34edb7db95a","image":"https://lh3.googleusercontent.com/-Vbm9mlgY6sU/WFwUL5gdUyI/AAAAAAAAEVw/QRqkCxvJl4w/220px-The_Face_of_a_Lupine_Blue.jpg?imgmax=1600","indexed_at":1690410782,"language":"en","published_at":1482429480,"reference":[],"summary":"Following
on from adding DNA barcodes to GBIF I''ve now uploaded a taxonomic classification
of DNA barcode BINs (Barcode Index Numbers). Each BIN is a cluster of similar
DNA barcodes that is essentially equivalent to a species. For more details
see: Ratnasingham, S., & Hebert, P. D. N. (2013, July 8). A DNA-Based Registry
for All Animal Species: The Barcode Index Number (BIN) System. (D. Fontaneto,
Ed.), PLoS ONE.","tags":["BOLD","DNA Barcoding","GBIF","Taxonomy"],"title":"DNA
barcoding taxonomy now in GBIF","updated_at":1482429492,"url":"https://iphylo.blogspot.com/2016/12/dna-barcoding-taxonomy-now-in-gbif.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/5pk2b-5k391","id":"4e94e10c-1585-4884-8c5e-2a76c1fc0f7f","image":null,"indexed_at":1690482385,"language":"en","published_at":1594992540,"reference":[],"summary":"This
morning, as part of a webinar on persistent identifiers, I gave a live demo
of a little toy to demonstrate linking together museum and herbaria specimens
with publications that use those specimens. A video of an earlier run through
of the demo appears below, for background on this demo see Diddling with semantic
data: linking natural history collections to the scientific literature.","tags":[],"title":"Persistent
Identifiers: A demo and a rant","updated_at":1594992559,"url":"https://iphylo.blogspot.com/2020/07/persistent-identifiers-demo-and-rant.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/qt5ae-kds17","id":"a77b249d-d2ce-4d22-a733-901d32043744","image":"https://lh3.googleusercontent.com/-Nix9hko4Mis/WDa9g9JD8AI/AAAAAAAAEUo/64SSPPPrY7M/170px-Copyright.svg.png?imgmax=1600","indexed_at":1690412638,"language":"en","published_at":1479155940,"reference":[],"summary":"Willi
Egloff, Donat Agosti, Puneet Kishor, David Patterson, and Jeremy A. Miller
have published an interesting preprint entitled \u201cCopyright and the Use
of Images as Biodiversity Data\u201d DOI:10.1101/087015 in which they argue
that taxonomic images aren''t copyrightable. I''m not convinced, and have
commented on the bioRxiv site.","tags":[],"title":"Copyright and the Use of
Images as Biodiversity Data","updated_at":1479982471,"url":"https://iphylo.blogspot.com/2016/11/copyright-and-use-of-images-as.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/t6fb9-4fn44","id":"8bc3fea6-cb86-4344-8dad-f312fbf58041","image":null,"indexed_at":1689954228,"language":"en","published_at":1639180860,"reference":[],"summary":"Markus
Strasser (@mkstra write a fascinating article entitled \"The Business of Extracting
Knowledge from Academic Publications\". I spent months working on domain-specific
search engines and knowledge discovery apps for biomedicine and eventually
figured that synthesizing \"insights\" or building knowledge graphs by machine-reading
the academic literature (papers) is *barely useful* :https://t.co/eciOg30Odc\u2014
Markus Strasser (@mkstra) December 7,","tags":["Ai","Business Model","Text
Mining"],"title":"The Business of Extracting Knowledge from Academic Publications","updated_at":1639180881,"url":"https://iphylo.blogspot.com/2021/12/the-business-of-extracting-knowledge.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/7b1b5-r2b55","id":"19145220-0ba1-4ee6-bed2-b2e86367e0c3","image":"https://lh3.googleusercontent.com/-53RPfncCGZs/VuxsNBOoHBI/AAAAAAAAEJM/Kq1HPJ1IHmU/Haniffia.png?imgmax=1600","indexed_at":1692994568,"language":"en","published_at":1458334740,"reference":[],"summary":"TL;DR;
The Plant List is now in GBIF http://doi.org/10.15468/btkum2. Readers of
this blog may recall that I''ve had a somewhat jaundiced view of The Plant
List.","tags":["DOI","GBIF","IPNI","Plant List"],"title":"The Plant List,
GBIF, and the primary literature","updated_at":1458334795,"url":"https://iphylo.blogspot.com/2016/03/the-plant-list-gbif-and-primary.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/v4g2y-95e02","id":"ad1b619c-7055-4f20-b3f5-fbfa33e99097","image":"http://www.morphbank.net?id=196637&imgType=thumb","indexed_at":1693669390,"language":"en","published_at":1233765960,"reference":[],"summary":"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.","tags":["GUI Ds","Semantic Web","Taxonomy","Wiki"],"title":"Wiki
demo","updated_at":1233767067,"url":"https://iphylo.blogspot.com/2009/02/wiki-demo.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/k5vrd-tae07","id":"02e30a68-6784-4501-a537-6fb945f3d84d","image":"https://lh3.googleusercontent.com/-dGuQKhH1gu0/V-5oJIf564I/AAAAAAAAESQ/0lVote3X0pk/bob_mesibov.jpg?imgmax=1600","indexed_at":1690482841,"language":"en","published_at":1594806420,"reference":[],"summary":"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?","tags":[],"title":"Darwin Core Million now twice a year","updated_at":1594806450,"url":"https://iphylo.blogspot.com/2020/07/darwin-core-million-now-twice-year.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/kcbnd-17a33","id":"e4fc03bc-1822-4d26-9eb3-eb30fda85fb7","image":"https://lh3.googleusercontent.com/-X50gPNWBhgM/WHZp0z6AurI/AAAAAAAAEWs/7sDEKYtHWdA/Screenshot%2525202017-01-11%25252016.30.57.png?imgmax=1600","indexed_at":1690417663,"language":"en","published_at":1484155320,"reference":[],"summary":"I''ve
added an experimental feature to BioStor that uses data from Wikidata and
Wikispecies to augment what information BioStor displays on authors.","tags":["BHL","Bio
Stor","Identiifers","ISNI","ORCID"],"title":"The Biodiversity Heritage Library
meets Wikidata via Wikispecies: adding author identifiers to BioStor","updated_at":1484395013,"url":"https://iphylo.blogspot.com/2017/01/the-biodiversity-heritage-library-meets.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/q0fy3-b1825","id":"ac0a8e76-4376-496d-bbc9-3d7d39237cf4","image":"http://ogc.gbif.org/wms?request=GetMap&bgcolor=0x666698&styles=,,&layers=gbif:country_fill,gbif:tabDensityLayer,gbif:country_borders&srs=EPSG:4326&filter=()(%3CFilter%3E%3CPropertyIsEqualTo%3E%3CPropertyName%3Eurl%3C/PropertyName%3E%3CLiteral%3E%3C![CDATA[http%3A%2F%2Fdata.gbif.org%2Fmaplayer%2Ftaxon%2F7225]]%3E%3C/Literal%3E%3C/PropertyIsEqualTo%3E%3C/Filter%3E)()&width=721&height=362&Format=image/png&bbox=-180,-90,180,90","indexed_at":1694225917,"language":"en","published_at":1348483320,"reference":[],"summary":"We
all have a \"past\" that we might not advertise widely, and my past includes
flirting with panbiogeography.","tags":["GBIF","Gondwana","Panbiogeography"],"title":"Towards
a biogeographic search engine","updated_at":1348484071,"url":"https://iphylo.blogspot.com/2012/09/towards-biogeographic-search-engine.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/vpk8f-a4m49","id":"046817ab-8442-44f1-8516-b462db838f03","image":null,"indexed_at":1693669968,"language":"en","published_at":1202143140,"reference":[],"summary":"Dave
Lunt has a nice post on How to visualize a phylogeny with thousands of tips?.
Dave lists 12 things that his ideal phylogenetic tree viewing tool should
do, and invites comments. It will be interesting to see what comes of this...","tags":[],"title":"How
to visualize a phylogeny with thousands of tips?","updated_at":1202143453,"url":"https://iphylo.blogspot.com/2008/02/how-to-visualize-phylogeny-with.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/py8nn-n1d68","id":"2d399a58-2ed0-47fe-9bb7-12b1a341a14d","image":null,"indexed_at":1693001739,"language":"en","published_at":1449009600,"reference":[],"summary":"For
those of you who, like me, weren''t at the \"Frontiers Of Biodiversity Informatics
and Modelling Species Distributions\" held at the AMNH in New York, here are
the videos of the talks and panel discussion, which the organisers have kindly
put up on Vimeo with the following description: The Center for Biodiversity
and Conservation (CBC) partnered with the Global Biodiversity Information
Facility (GBIF) to host a special \"Symposium and Panel Dis","tags":["AMNH","GBIF","Video"],"title":"Frontiers
of biodiversity informatics and modelling species distributions #GBIFfrontiers
@AMNH videos","updated_at":1449009627,"url":"https://iphylo.blogspot.com/2015/12/frontiers-of-biodiversity-informatics.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/h1mwa-71h17","id":"e91e9b25-206c-4c22-8f42-2efdd0348a7a","image":"https://lh3.googleusercontent.com/-pGfIUu6vvKY/VrIiuUt3FQI/AAAAAAAAEHA/1kq9zRiU3fY/museum.png?imgmax=800","indexed_at":1692988981,"language":"en","published_at":1454514900,"reference":[],"summary":"@sckottie
@rdmpage @christgendreau Three small, early adopting projects should show
expected network of synergies if JSON-LD actually useful\u2014 David Shorthouse
(@dpsSpiders) February 1, 2016 In a recent Twitter conversation including
David Shorthous and myself (and other poor souls who got dragged in) we discussed
how to demonstrate that adopting JSON-LD as a simple linked-data friendly
format might help bootstrap the long awaited \"biodiversit","tags":["Crossref","JSON-LD","Knowledge
Graph","Linked Data","NCBI"],"title":"Bootstrapping the biodiversity knowledge
graph with JSON-LD","updated_at":1454514907,"url":"https://iphylo.blogspot.com/2016/02/bootstrapping-biodiversity-knowledge.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/1wa3h-65b96","id":"97527b74-721b-4e78-a4a8-fff6b7963374","image":"https://lh3.googleusercontent.com/-cVV_ID0oeJI/V3Ucox8EsZI/AAAAAAAAEO0/F8qHW0lbKa8/Screenshot%2525202016-06-30%25252012.30.53.png?imgmax=1600","indexed_at":1690425475,"language":"en","published_at":1467292920,"reference":[],"summary":"In
the previous post I sketched out a workflow to annotate articles using hypothes.is
and aggregate those annotations.","tags":["Annotation","Hackathon","Hypothes
Is","Knowledge Graph","Re Con 16"],"title":"Aggregating annotations on the
scientific literature: a followup on the ReCon16 hackday","updated_at":1467292943,"url":"https://iphylo.blogspot.com/2016/06/aggregating-annotations-on-scientific_30.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/3c15d-m1z78","id":"7543a6b8-0845-41e0-b812-d0a15264fb2e","image":"https://lh3.googleusercontent.com/-5FaxDZeQAtE/V2q2_yE3EpI/AAAAAAAAEN4/W3Em4l2J0oc/links1.png?imgmax=1600","indexed_at":1690427750,"language":"en","published_at":1466611440,"reference":[],"summary":"The
last few days I''ve been re-reading articles about Ted Nelson''s work (including
ill-fated Project Xanadu), reading articles celebrating his work (brought
together in the open access book \"Intertwingled\"), playing with Hypothes.is,
and thinking about annotation and linking.","tags":["Hypothes Is","Xanadu"],"title":"What
happens when open access wins?","updated_at":1466697964,"url":"https://iphylo.blogspot.com/2016/06/what-happens-when-open-access-wins.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/94181-tqv10","id":"260eeb82-ec5e-4fe7-b9b6-2da33305f387","image":null,"indexed_at":1690427050,"language":"en","published_at":1464257220,"reference":[],"summary":"I''ll
be taking a break shortly, so I thought I''d try to gather some thoughts on
a few projects/ideas that I''m working on. These are essentially extended
notes to myself to jog my memory when I return to these topics. BOLD
data into GBIF Following on from work on getting mosquito data into
GBIF I''ve been looking at DNA barcoding data. BOLD data is mostly absent
from GBIF.","tags":[],"title":"Notes on current and future projects","updated_at":1464262365,"url":"https://iphylo.blogspot.com/2016/05/notes-on-current-and-future-projects.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/y54eq-qbd84","id":"35f6bc16-4d10-4f78-9caa-05c51ab4ed03","image":"https://lh3.googleusercontent.com/-lIlsxjpgRWY/VzHhbwbricI/AAAAAAAAEM4/zWsZ-usbbHU/Screenshot%2525202016-05-10%25252013.52.09.png?imgmax=1600","indexed_at":1692990863,"language":"en","published_at":1462886760,"reference":[],"summary":"Some
notes to self about future directions for the \"million DNA barcodes map\"
http://iphylo.org/~rpage/bold-map/. At the moment we have an interactive
map that we can pan and zoom, and click on a marker to get a list of one or
more barcodes at the location. We can also filter by major taxonomic group.
Here are some ideas on what could be next. Search At the
moment search is simply browsing the map.","tags":["DNA Barcoding","Maps","Phylogeny"],"title":"Notes
on next steps for the million DNA barcodes map","updated_at":1462886777,"url":"https://iphylo.blogspot.com/2016/05/notes-on-next-steps-for-million-dna.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/cd5mt-cbk37","id":"c3c9401e-2f12-4288-9e4c-2e2a9e77cb36","image":"http://lh3.ggpht.com/-DNwCildW1WE/UEuMkbCKUuI/AAAAAAAAB1I/OiIMrYSppeI/photo.PNG?imgmax=800","indexed_at":1694230976,"language":"en","published_at":1347128460,"reference":[],"summary":"The
release of the ENCODE (ENCyclopedia Of DNA Element) project has generated
much discussion (see Fighting about ENCODE and junk). Perhaps perversely,
I''m more interested in the way Nature has packaged the information
than the debate about how much of our DNA is \"junk.\" Nature has
a website (http://www.nature.com/encode/) that demonstrates the use of \"threads\"
to navigate through a set of papers.","tags":["ENCODE","E Pub","I Pad","Nature","Ted
Nelson"],"title":"Decoding Nature''s ENCODE iPad app - OMG it''s full of ePUB","updated_at":1347128555,"url":"https://iphylo.blogspot.com/2012/09/decoding-nature-encode-ipad-app-omg-it.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/6ct8h-wm857","id":"8c6833ab-c027-46cf-bb24-fb7c5700c038","image":"http://3.bp.blogspot.com/_Gct8lVAxKqQ/SYbScMfWTNI/AAAAAAAAAZ4/kb7_2NlrepQ/s320/Untitled.png","indexed_at":1693672019,"language":"en","published_at":1233570780,"reference":[],"summary":"Last
night BBC One aired David Attenborough''s Charles Darwin and the Tree of Life,
which featured a lovely \"fly through\" the tree of life:In conjunction with
the TV show, the Wellcome Trust has launched the Interactive Tree of Life,
a Flash-based view of the tree of life. There''s also a blog about the project.
Here''s a demo of the tree:The tree looks very nice, and a lot of work has
gone into it, but I am somewhat underwhelmed.","tags":["BBC","Creative Commons","Phylogeny","Tree
Of Life","Visualisation"],"title":"Thoughts on the Wellcome Interactive Tree
of Life","updated_at":1233573030,"url":"https://iphylo.blogspot.com/2009/02/thoughts-on-wellcome-interactive-tree.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/cybn5-ded07","id":"8de27870-94f4-4af9-b6e0-060650848a20","image":null,"indexed_at":1692988462,"language":"en","published_at":1461226740,"reference":[],"summary":"One
of my frustrations with the GBIF portal is that it is hard to drill down and
search in a specific area. You have to zoom in and then click for a list of
occurrences in the current bounding box of the map. You can''t, for example,
draw a polygon such as the boundary of a protected area and search within
that area.","tags":["GBIF","Leaflet","Search"],"title":"Searching GBIF by
drawing on a map","updated_at":1461226754,"url":"https://iphylo.blogspot.com/2016/04/searching-gbif-by-drawing-on-map.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/p0bf4-qbb95","id":"36f9116b-c860-4ea3-abbb-0bdc2781f6ca","image":null,"indexed_at":1693672485,"language":"en","published_at":1232018160,"reference":[],"summary":"Yes,
I know this is ultimately a case of the \"genius of and\", but the more I
play with the Semantic Mediawiki extension the more I think this is going
to be the most productive way forward. I''ve had numerous conversations with
Vince Smith about this. Vince and colleagues at the NHM have been doing a
lot of work on \"Scratchpads\" -- Drupal based webs sites that tend to be
taxon-focussed.","tags":["Mediawiki","Scratchpads"],"title":"Wikis versus
Scratchpads","updated_at":1232019681,"url":"https://iphylo.blogspot.com/2009/01/wikis-versus-scratchpads.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/gy6w3-vpy86","id":"3161cd0a-a798-414b-9477-f9ad7796458f","image":"https://lh3.googleusercontent.com/-IteOIhEs1LI/WaNiQvAyxDI/AAAAAAAAEfQ/GdXbMdgoumEV0WieDx-ZOpHxmceT3oRbwCHMYCw/journal.pbio.2002231.g001.PNG?imgmax=1600","indexed_at":1690496676,"language":"en","published_at":1503879720,"reference":[],"summary":"Let\u2019s
rise up to unite taxonomy and technology - I thought it already was?","tags":["Biodiversity
Informatics","Holly Bik","I Species","P Lo S"],"title":"Let\u2019s rise up
to unite taxonomy and technology","updated_at":1503879750,"url":"https://iphylo.blogspot.com/2017/08/lets-rise-up-to-unite-taxonomy-and.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/fcbvh-geg90","id":"a1f96c24-53f8-4469-9f37-344cd6449ece","image":"https://lh3.googleusercontent.com/-Rus4m2eKuBs/WvM1se2JQWI/AAAAAAAAEps/rJc3c8DWPqY7csFf3WD_nzvTL5nIYXSDACHMYCw/s0/taxonomist_map.png","indexed_at":1690497178,"language":"en","published_at":1525888380,"reference":[],"summary":"David
Shorthouse (@dpsspiders) makes some very cool things, and his latest project
World Taxonomists & Systematists is a great example of using automation to
assemble a list of the world''s taxonomists and systematists. The project
uses ORCID.","tags":["Andy Mabbett","David Shorthouse","ORCID","Wikidata"],"title":"World
Taxonomists and Systematists via ORCID","updated_at":1525888436,"url":"https://iphylo.blogspot.com/2018/05/world-taxonomists-and-systematists-via.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/bsreb-ky953","id":"dad722b3-3a94-42cf-a546-48a1f0ebd955","image":"http://4.bp.blogspot.com/_Gct8lVAxKqQ/ST5lSHyTmvI/AAAAAAAAAZQ/nOVNu-tQEOg/s320/lens1.png","indexed_at":1693674235,"language":"en","published_at":1228821480,"reference":[],"summary":"Among
the many weaknesses of my challenge demo is the way it simply dumps out a
list of sequences (see comments on the demo.","tags":["Table Lens","Matrix","Table","Visualisation"],"title":"Table
lens view of data matrix","updated_at":1228827442,"url":"https://iphylo.blogspot.com/2008/12/table-lens-view-of-data-matrix.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/44ber-48595","id":"3dee7375-db7b-4cc1-9b0a-d053dc74deed","image":"https://lh3.googleusercontent.com/-I-vPn-tb6Yo/V-5kX-q6yBI/AAAAAAAAESE/b-XBde1r1Nk/Screenshot%2525202016-09-30%25252014.01.05.png?imgmax=1600","indexed_at":1690421342,"language":"en","published_at":1475241000,"reference":[],"summary":"The
GBIF 2016 Ebbe Nielsen Challenge has received 15 submissions. You can view
them here: Unlike last year where the topic was completely open, for the second
challenge we''ve narrowed the focus to \"Analysing and addressing gaps and
biases in primary biodiversity data\". As with last year, judging is limited
to the jury (of which I''m a member), however anyone interested in biodiversity
informatics can browse the submissions.","tags":["Challenge","GBIF"],"title":"GBIF
2016 Ebbe Nielsen Challenge entries","updated_at":1475241058,"url":"https://iphylo.blogspot.com/2016/09/gbif-2016-ebbe-nielsen-challenge-entries.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/f5x4y-8w261","id":"574ec9ba-7927-497c-a2c4-384f2ba33aaf","image":"http://ci.nii.ac.jp/jp/images/top_h_logo.gif","indexed_at":1693673581,"language":"en","published_at":1220016420,"reference":[],"summary":"In
case I forget how to do this, and as an example of how easy it is to get sucked
into a black hole of programming micro-details, I spent a hour or more trying
to figure out how to handle Japanese characters.I''m building a database of
publications linked to taxonomic names, and I''m interested in linking to
electronic versions of those publications.","tags":["Encoding","Japanese","Open
URL","Programming","UTF 8"],"title":"Turning Japanese: EUC-JP, UTF-8, and
percent-encoding","updated_at":1220086923,"url":"https://iphylo.blogspot.com/2008/08/turning-japanese-euc-jp-utf-8-and.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/xdv05-ewp28","id":"783d0856-65b5-4517-a8fe-bdde583c440b","image":null,"indexed_at":1692986653,"language":"en","published_at":1460714160,"reference":[],"summary":"As
part of BHL''s \"Celebrating 10 years of inspiring discovery through free
access to biodiversity knowledge\" at the NHM and Kew Gardens in London, I
was interviewed by Martin Kalfatovic (@UDCMRK). We chatted about BHL, the
work I''ve been doing on BioStor, and the future of BHL.","tags":["BHL","Impact","Interview"],"title":"The
Biodiversity Heritage Library at 10: Let''s talk impact interview by @UDCMRK","updated_at":1460714218,"url":"https://iphylo.blogspot.com/2016/04/the-biodiversity-heritage-library-at-10.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/6zzw6-fx070","id":"2704d127-b31a-4312-8139-6fcdf8c8c930","image":"http://lh3.ggpht.com/-fDQXVuaQos0/T_DSKI_eU_I/AAAAAAAABdM/6jvYSwqdmXY/gbif360x180.png?imgmax=800","indexed_at":1694246686,"language":"en","published_at":1341182520,"reference":[],"summary":"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.","tags":["Equirectangular Projection","Github","Maps","Orthographic
Projection","Polar"],"title":"Using orthographic projections to map organism
distributions","updated_at":1341182563,"url":"https://iphylo.blogspot.com/2012/07/using-orthographic-projections-to-map.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/xpce1-ggg07","id":"8d4bf59c-7bc7-409f-9738-674dcadaeef3","image":null,"indexed_at":1690500214,"language":"en","published_at":1507146060,"reference":[],"summary":"I
gave a \"wild ideas\" talk at TDWG17 suggesting that the biodiversity community
use Bitcoin to make micropayments to use data.","tags":["Bitcoin","Micropayment","TDWG"],"title":"Bitcoin,
biodiversity, and micropayments for open data","updated_at":1507146101,"url":"https://iphylo.blogspot.com/2017/10/bitcoin-biodiversity-and-micropayments.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/snnd5-9pa62","id":"805c4d16-55e9-468a-ae32-609c9725d2bd","image":"http://lh6.ggpht.com/-40TNwnPVXuU/T9jEbCMx2BI/AAAAAAAABac/uv-JsgnfZNs/cluster-map-details.png?imgmax=800","indexed_at":1694252588,"language":"en","published_at":1339606080,"reference":[],"summary":"As
part of a project to build a tool to navigate through taxonomic names and
classifications I''ve become interested in quick ways to compare classifications.","tags":["Classification","Cluster
Maps","Demansia","EOL","Visualisation"],"title":"Visualising differences between
classifications using cluster maps","updated_at":1339606137,"url":"https://iphylo.blogspot.com/2012/06/visualising-differences-between.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/snysf-6p568","id":"94ca6e37-3398-4244-9a1d-f7363c80523a","image":null,"indexed_at":1692991393,"language":"en","published_at":1457011560,"reference":[],"summary":"Last
week (25-26 February) I was in London for CISCO Pit Stop event.","tags":["Cisco","Digitisation","NHM","Pit
Stop","Talk"],"title":"Cisco Pit Stop: Digitising the Natural History Museum\u2019s
collections","updated_at":1457011742,"url":"https://iphylo.blogspot.com/2016/03/cisco-pit-stop-digitising-natural.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/rfzrb-pgz89","id":"60588d25-e10f-4b84-81f7-15d2c95eb903","image":"https://lh3.googleusercontent.com/-XY78tBNWacA/VwdfcSPIWUI/AAAAAAAAEJ8/hKkSNIC-4MQ/E2asamsw.png?imgmax=1600","indexed_at":1692990229,"language":"en","published_at":1460100960,"reference":[],"summary":"After
experimenting with a dynamic, online version of my notes \"Towards a biodiversity
knowledge graph\" I''ve published a static version in RIO: doi:10.3897/rio.2.e8767.","tags":[],"title":"Towards
a biodiversity knowledge graph now in RIO","updated_at":1460100983,"url":"https://iphylo.blogspot.com/2016/04/towards-biodiversity-knowledge-graph.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/ave51-v2f79","id":"78545fc6-d268-4d08-8c55-04466c6fecc7","image":null,"indexed_at":1693675437,"language":"en","published_at":1229014500,"reference":[],"summary":"The
Science Commons has released a short video by Jesse Dylan, who made the Yes
We Can video.","tags":["Creative Commons","Science Commons"],"title":"Yes
We Can - \"scientists are the ultimate remixers\"","updated_at":1229015010,"url":"https://iphylo.blogspot.com/2008/12/yes-we-can-scientists-are-ultimate.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/p7r0x-kb326","id":"99201868-7581-42d1-af1b-49a76291faec","image":"http://lh6.ggpht.com/-gzyEUIOdQHE/T5ZV6r8tdWI/AAAAAAAABMY/ueWxb18xC-E/obsolete.png?imgmax=800","indexed_at":1694261063,"language":"en","published_at":1335252420,"reference":[],"summary":"Dark
taxa have become even darker. NCBI has pulled the plug on large numbers of
DNA barcode sequences that lack scientific names. For example, taxon Cyclopoida
sp. BOLD:AAG9771 (tax_id 818059) now has a sparse page that has no associated
sequences. From an earlier download of EMBL I know that this taxon is associated
with at least 5 sequences, such as GU679674. But if you go to that sequence
you get this:So the the sequence is hidden.","tags":["Dark Taxa","DNA Barcoding","NCBI"],"title":"Dark
taxa even darker: NCBI pulls (some) DNA barcodes from GenBank (updated)","updated_at":1335284034,"url":"https://iphylo.blogspot.com/2012/04/dark-taxa-even-darker-ncbi-pulls-dna.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/ehbwx-fjv34","id":"d8604d2a-9f51-45e3-afa0-84ee6f238a89","image":"http://lh3.ggpht.com/-rHOMhlnCMLo/T0upivhNFBI/AAAAAAAABKc/yGXlUbSH6XI/fmnh147942.png?imgmax=800","indexed_at":1694266378,"language":"en","published_at":1330358640,"reference":[],"summary":"Following
on from exploring links between GBIF and GenBank here I''m going to look at
links between GBIF and the primary literature, in this case articles scanned
by the Biodiversity Heritage Library (BHL). The OCR text in BHL can be mined
for a variety of entities. BHL itself has used uBio''s tools to identity taxonomic
names in the OCR text, and in my BioStor project I''ve extracted article-level
metadata and geographic co-ordinates.","tags":["BHL","Bio Stor","GBIF","Identifiers","Linking"],"title":"Linking
GBIF and the Biodiversity Heritage Library","updated_at":1330358671,"url":"https://iphylo.blogspot.com/2012/02/linking-gbif-and-biodiversity-heritage.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/kw4vt-rzg34","id":"e5b82be6-72be-4ae9-911e-6083cb485513","image":"http://4.bp.blogspot.com/_Gct8lVAxKqQ/SS21JCEI0uI/AAAAAAAAAZI/lYe7MprQqEc/s200/carmen.png","indexed_at":1693675991,"language":"en","published_at":1227732000,"reference":[],"summary":"One
byproduct of playing with the Challenge Demo is that I come across some rather
surprising results.","tags":["Bryozoa","Carmen Electra","Challenge","Error"],"title":"Sequencing
Carmen Electra","updated_at":1227732927,"url":"https://iphylo.blogspot.com/2008/11/sequencing-carmen-electra.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/7h9kf-cgh02","id":"4dc9da98-9594-42cd-9e82-2a0fdcf4ecdc","image":null,"indexed_at":1690510742,"language":"en","published_at":1507037580,"reference":[],"summary":"Some
random notes on the first day of TDWG 2017. First off, great organisation
with the first usable conference calendar app that I''ve seen (https://tdwg2017.sched.com). I
gave the day''s keynote address in the morning (slides below).
Towards a biodiversity knowledge graph from Roderic Page It
was something of a stream of consciousness brain dump, and tried to cover
a lot of (maybe too much) stuff.","tags":["BHL","GBIF","Knowledge Graph","Linked
Data","TDWG"],"title":"TDWG 2017: thoughts on day 1","updated_at":1507037626,"url":"https://iphylo.blogspot.com/2017/10/tdwg-2017-thoughts-on-day-1.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/s2ttc-w0z21","id":"60e3c6e8-da83-467c-ba06-ba7817a2876c","image":null,"indexed_at":1694268242,"language":"en","published_at":1329903540,"reference":[],"summary":"I''ll
keep this short: LSIDs suck because they are so hard to set up that many LSIDs
don''t actually work. Because of this there seems to be no shame in publishing
\"fake\" LSIDs (LSIDs that look like LSIDs but which don''t resolve using
the LSID protocol). Hey, it''s hard work, so let''s just stick them on a web
page but not actually make them resolvable.","tags":["LSID","Rant"],"title":"Why
LSIDs suck","updated_at":1329903568,"url":"https://iphylo.blogspot.com/2012/02/why-lsids-suck.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/hj161-hh554","id":"c53cd9ef-15cc-443e-8044-8c9f30754743","image":"http://lh4.ggpht.com/-lWaePnxJpZo/T0NyWoKWQaI/AAAAAAAABJg/R-Q5YOG6--E/density.png?imgmax=800","indexed_at":1694268908,"language":"en","published_at":1329820260,"reference":[],"summary":"As
part of my mantra that it''s not about the data, it''s all about the links
between the data, I''ve started exploring matching GenBank sequences to GBIF
occurrences using the specimen_voucher codes recorded in GenBank sequences.
It''s quickly becoming apparent that this is not going to be easy.","tags":["Frogs","GBIF","Genbank","Geophylogeny","KML"],"title":"Linking
GBIF and Genbank","updated_at":1329821040,"url":"https://iphylo.blogspot.com/2012/02/linking-gbif-and-genbank.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/jpph3-ztv21","id":"33f8adf2-b1e1-4ce2-ae1b-ef16e4dd557d","image":"http://lh5.ggpht.com/-Lr2pXxmODc4/TzUNWFxnRNI/AAAAAAAABI4/BYGxFfSBe9M/blastmap.png?imgmax=800","indexed_at":1694269985,"language":"en","published_at":1328876880,"reference":[],"summary":"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.","tags":["BLAST","Dark
Taxa","Phyloinformatics"],"title":"BLAST a sequence and get a tree and a map","updated_at":1328876890,"url":"https://iphylo.blogspot.com/2012/02/blast-sequence-and-get-tree-and-map.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/tj6t6-ak763","id":"a2e0943c-692c-4d9b-b406-4acb5075c85e","image":"http://4.bp.blogspot.com/_Gct8lVAxKqQ/SSpr8W_KHII/AAAAAAAAAYo/cGeX86R2lok/s320/frogs.png","indexed_at":1693676591,"language":"en","published_at":1227516300,"reference":[],"summary":"One
of the things I''ve struggled with most in putting together a web site for
the challenge is how to summarise that taxonomic content of a study. Initially
I was playing with showing a subtree of the NCBI taxonomy, highlighting the
taxa in the study. But this assumes the user is familiar with the scientific
names of most of life. I really wanted something that tells you \"at a glance\"
what the study is about.","tags":["Challenge","Treemap","Visualisation"],"title":"What
is a study about? Treemaps of taxa","updated_at":1227518779,"url":"https://iphylo.blogspot.com/2008/11/what-is-study-about-treemaps-of-taxa.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/kddq9-knb87","id":"06485682-3c8a-4bb1-9730-319e552e82a3","image":"https://lh3.googleusercontent.com/-V13f764Va5M/VfvoGnw-vuI/AAAAAAAAEDA/Q5kjK6jeGCU/slide.png?imgmax=800","indexed_at":1692998581,"language":"en","published_at":1442572320,"reference":[],"summary":"Currently
in classes where I teach the basics of tree building, we still fire up ancient
iMacs, load up MacClade, and let the students have a play. Typically we give
them the same data set and have a class competition to see which group can
get the shortest tree by manually rearranging the branches. It\u2019s fun,
but the computers are old, and what\u2019s nostalgic for me seems alien to
the iPhone generation.","tags":["Mac Clade","Phylogeny","Teaching","Touch"],"title":"Towards
an interactive web-based phylogeny editor (\u00e0 la MacClade)","updated_at":1454592702,"url":"https://iphylo.blogspot.com/2015/09/towards-interactive-web-based-phylogeny.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/y5dva-nmc23","id":"c653a893-34c5-4297-8bd9-ed0c1766a949","image":null,"indexed_at":1694272981,"language":"en","published_at":1326990900,"reference":[],"summary":"As
part of a course on \"phyloinformatics\" that I''m about to teach I''ve been
making some visualisations of classifications. Here''s one I''ve put together
using jQuery Mobile and the Encyclopedia of Life API. It''s pretty limited,
but is a simple way to explore EOL using three different classifications.","tags":["API","EOL","I
Pad","J Query Mobile"],"title":"EOL iPad web app using jQueryMobile","updated_at":1326990917,"url":"https://iphylo.blogspot.com/2012/01/eol-ipad-web-app-using-jquerymobile.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/7621m-t9b65","id":"d776eeb7-9554-40b0-9333-0ba5ec92bce2","image":"https://lh3.googleusercontent.com/-i6RdZ9f7CsU/VnLWdz1uUEI/AAAAAAAAEF0/-BrevKnTYo0/fault-tolerance.png?imgmax=800","indexed_at":1693000389,"language":"en","published_at":1450366560,"reference":[],"summary":"OK,
so the title is pure click bait, but here''s the thing. It seems to me that
the Semantic Web as classically conceived (RDF/XML, SPARQL, triple stores)
has had relatively little impact outside academia, whereas other technologies
such as JSON, NoSQL (e.g., MongoDB, CouchDB) and graph databases (e.g., Neo4J)
have got a lot of developer mindshare. In biodiversity informatics the Semantic
Web has been a round for a while.","tags":["Couch DB","ElasticSearch","Human
Trafficking","JSON-LD","Neo 4 J"],"title":"Will JSON, NoSQL, and graph databases
save the Semantic Web?","updated_at":1450366588,"url":"https://iphylo.blogspot.com/2015/12/will-json-nosql-and-graph-databases.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/q6yw5-5vr33","id":"edfa9706-41e4-4162-9a51-58f4bc95e345","image":null,"indexed_at":1694278374,"language":"en","published_at":1321968480,"reference":[],"summary":"Quick
note to self in case I (inevitably) forget later. If you are using Apache
mod_rewrite to make nice, clean URLs, and are also supporting JSONP, you may
run into the situation where you have code that wants to append \"?callback=xxx\"
to your URL (e.g., a cross-domain AJAX call in jQuery). Imagine you have a
nice clean URL /user/123, which actually corresponds to user.php?id=123.","tags":["Apache","J
Query","JSONP","Mod Rewrite","Stackoverflow"],"title":"Apache mod_rewrite
and question marks \"?\"","updated_at":1321968498,"url":"https://iphylo.blogspot.com/2011/11/quick-note-to-self-in-case-i-inevitably.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/xqb1n-xh905","id":"64be7d4e-80dc-447b-90fb-96f586b9a03c","image":"https://lh3.googleusercontent.com/-rrpRKGbMfmU/Va-a080CEpI/AAAAAAAAD9w/3fkk0z-H3sI/JSTOR_Logo_RGB_60x76.gif?imgmax=800","indexed_at":1692998110,"language":"en","published_at":1437571800,"reference":[],"summary":"Browsing
JSTOR''s Global Plants database I was struck by the number of comments people
have made on individual plant specimens. For example, for the Holotype of
Scorodoxylum hartwegianum Nees (K000534285) there is a comment from
H\u00e5kan Wittzell that the \"Collection number should read 1269 according
to Plantae Hartwegianae\". In JSTOR the collection number is 1209. Now, many
(if not all) of these specimens will also be in GBIF.","tags":["Altmetric","Annotation","Disqus","GBIF","JSTOR"],"title":"Altmetrics,
Disqus, GBIF, JSTOR, and annotating biodiversity data","updated_at":1437571927,"url":"https://iphylo.blogspot.com/2015/07/altmetrics-disqus-and-annotating.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/stfbb-b5744","id":"113c581d-7300-4efd-80de-1a10ca80a5d8","image":"http://lh3.ggpht.com/-QmCQYqFQdS4/TsZq07Fh2GI/AAAAAAAABDM/LoclO4DZQ2g/gallica.png?imgmax=800","indexed_at":1694279036,"language":"en","published_at":1321626300,"reference":[],"summary":"Recently
I''ve been thinking about the best ways to make article-level metadata from
BioStor more widely available. For example, for someone visiting the BHL site
there is no easy way to find articles, which are the basic unit for much of
the scientific literature. How hard would it be to add articles to BHL?","tags":["Articles","BHL","Bio
Stor","Gallica","Google Books"],"title":"Adding article-level metadata to
BHL","updated_at":1321626333,"url":"https://iphylo.blogspot.com/2011/11/recently-ive-been-thinking-about-best.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/n86f3-zxv91","id":"cc0f612a-0d80-4a3d-bff8-5310eb94c0e3","image":"https://lh3.googleusercontent.com/-nZmxFt1E4qo/VbY8hL4eFTI/AAAAAAAAD-g/ozw1tTEPmHA/626ce1b38c2b42f77802e4e8c597820e_400x400.jpeg?imgmax=800","indexed_at":1693005364,"language":"en","published_at":1438006380,"reference":[],"summary":"In
my (previous post ) I discussed the potential for the Biodiversity Data Journal
(BDJ) to be a venue for nano (or near-nano publications). In this post I want
to draw attention to what I think is a serious stumbling block, which is the
lack of machine readable statements in the journal.","tags":[],"title":"The
Biodiversity Data Journal is not machine readable","updated_at":1438006431,"url":"https://iphylo.blogspot.com/2015/07/the-biodiversity-data-journal-is-not.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/s89h9-mda18","id":"87ff5ec4-2a9d-417e-8d78-1ee4079451c5","image":null,"indexed_at":1693677844,"language":"en","published_at":1215705840,"reference":[],"summary":"Interesting
paper by Huss et al. in PLoS Biology entitled \"A Gene Wiki for Community
Annotation of Gene Function\" (doi:10.1371/journal.pbio.0060175). Essentially,
the paper describes using Wikipedia to create a comprehensive gene wiki:In
principle, a comprehensive gene wiki could have naturally evolved out of the
existing Wikipedia framework, and as described above, the beginnings of this
process were already underway.","tags":["EOL","Wikipedia"],"title":"Why isn''t
EOL using Wikipedia?","updated_at":1215706561,"url":"https://iphylo.blogspot.com/2008/07/why-isnt-eol-using-wikipedia.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/rtx14-m7596","id":"0b3fea52-d35c-49b9-b881-a970d616f574","image":"https://lh3.googleusercontent.com/-olxAhunC_Dw/VbY8d_H8CzI/AAAAAAAAD-Y/_leHwprgc8k/626ce1b38c2b42f77802e4e8c597820e_400x400.jpeg?imgmax=800","indexed_at":1693014616,"language":"en","published_at":1437999180,"reference":[],"summary":"I
stumbled across this intriguing paper: Do, L., & Mobley, W. (2015, July 17).
Single Figure Publications: Towards a novel alternative format for scholarly
communication. F1000Research. F1000 Research, Ltd.","tags":["Annotation","Biodiversity
Data Journal","Nanopublication"],"title":"Nanopublications and annotation:
a role for the Biodiversity Data Journal?","updated_at":1438006395,"url":"https://iphylo.blogspot.com/2015/07/nanopublications-and-annotation-role.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/n20vx-a4930","id":"065a9caa-086d-47de-ab3e-0d5385770b15","image":null,"indexed_at":1693008720,"language":"en","published_at":1438691880,"reference":[],"summary":"Note
to self about a possible project. This PLoS ONE paper: Tib\u00e9ly, G., Pollner,
P., Vicsek, T., & Palla, G. (2013, December 31). Extracting Tag Hierarchies.
(P. Csermely, Ed.)PLoS ONE.","tags":["Folksonomy","Machine Learning","Note
To Self","Possible Project","Tags"],"title":"Possible project: extract taxonomic
classification from tags (folksonomy)","updated_at":1438691939,"url":"https://iphylo.blogspot.com/2015/08/possible-project-extract-taxonomic.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/sx242-7wv17","id":"11776cfd-a863-49c5-b8fa-0708ba5fc3fc","image":"https://lh3.googleusercontent.com/-A99btr6ERMs/Vl1Wvjp2OtI/AAAAAAAAEFI/7bKdRjNG5w0/ytNkVT2U.jpg?imgmax=800","indexed_at":1690415576,"language":"en","published_at":1473232140,"reference":[],"summary":"This
guest post by Tony Rees describes his quest to track all genus names ever
published (plus a subset of the species\u2026). A \u201choly grail\u201d for
biodiversity informatics is a suitably quality controlled, human- and machine-queryable
list of all the world\u2019s species, preferably arranged in a suitable taxonomic
hierarchy such as kingdom-phylum-class-order-family-genus or other.","tags":["Guest
Post","IRMNG","Tony Rees"],"title":"Guest post: Absorbing task or deranged
quest: an attempt to track all genus names ever published","updated_at":1473258854,"url":"https://iphylo.blogspot.com/2016/09/guest-post-absorbing-task-or-deranged.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/m9y3y-bpc11","id":"c521d4ce-2289-4d21-9fa0-4ea7d8ae14f0","image":"https://lh3.googleusercontent.com/-N6AXbsRoMCM/VYwRlsArr7I/AAAAAAAAD8k/MnbBoFdV2YA/dwca.png?imgmax=800","indexed_at":1693013394,"language":"en","published_at":1435242900,"reference":[{"key":"ref1","url":"http://eol.org/pages/38177334/literature"}],"summary":"Two
ongoing challenges in biodiversity informatics are getting data into a form
that is usable, and linking that data across different projects platforms.
A recent and interesting approach to this problem are \"data journals\" as
exemplified by the Biodiversity Data Journal. I''ve been exploring some data
from this journal that has been aggregated by GBIf and EOL, and have come
across a few issues.","tags":["Biodiversity Data Journal","Darwin Core Archive","EOL","GBIF","Pensoft"],"title":"Biodiversity
Data Journal data lost on the way to GBIF and EOL","updated_at":1435242916,"url":"https://iphylo.blogspot.com/2015/06/biodiversity-data-journal-data-lost-on.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/q72m8-z7859","id":"98faf9a0-6903-4bd1-8b45-9a3b39651403","image":"https://lh3.googleusercontent.com/-U2AGskKg_dU/V8WfP75AcOI/AAAAAAAAERM/nfQ33C_wduM/singlefig_98253.jpg.png?imgmax=1600","indexed_at":1690419140,"language":"en","published_at":1472569140,"reference":[],"summary":"David
Schindel and colleagues recently published a paper in the Biodiversity
Data Journal: Schindel, D., Miller, S., Trizna, M., Graham, E., & Crane,
A. (2016, August 26). The Global Registry of Biodiversity Repositories: A
Call for Community Curation. BDJ. Pensoft Publishers.","tags":["Community","Curation","Gr
Bio","Wikidata"],"title":"GRBio: A Call for Community Curation - what community?","updated_at":1472569155,"url":"https://iphylo.blogspot.com/2016/08/grbio-call-for-community-curation-what.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/bqe4h-2ek08","id":"7d74761d-3ae0-498b-aba8-6d11bbe75213","image":"http://lh5.ggpht.com/-7W6c0wSashI/VP7I_diRNcI/AAAAAAAADsM/uPJCz3La7zs/submissions.png?imgmax=800","indexed_at":1692829500,"language":"en","published_at":1425983700,"reference":[],"summary":"The
GBIF Ebbe Nielsen Challenge has closed and we have 23 submissions for the
jury to evaluate. There''s quite a range of project types (and media, including
sound and physical objects), and it''s going to be fascinating to evaluate
all the entries (some of which are shown below). This is the first time GBIF
has run this challenge, so it''s gratifying to see so much creativity in response
to the challenge.","tags":["Challenge","GBIF"],"title":"GBIF Ebbe Nielsen
Challenge submissions: judging begins","updated_at":1425983755,"url":"https://iphylo.blogspot.com/2015/03/gbif-ebbe-nielsen-challenge-submissions.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/xvdw8-nc818","id":"f8b68a35-e748-4f50-9a86-e27da69974d6","image":"http://lh3.googleusercontent.com/-bVM7FyjKhH4/VVsTLrQJxOI/AAAAAAAADvc/w8oaaWSYaj4/class.EMuMedia.php.jpeg?imgmax=800","indexed_at":1692830574,"language":"en","published_at":1432032000,"reference":[],"summary":"Text
mining for museum specimen identifiers #TDM http://t.co/BsFXSAZJpK cc @rdmpage
@robgural thoughts?\u2014 Ross Mounce (@rmounce) May 19, 2015 This post
is a response to Ross Mounce''s post Text mining for museum specimen identifiers.","tags":["Ross
Mounce","Specimen Codes","Text Mining"],"title":"Text mining for museum specimen
identifiers","updated_at":1432032056,"url":"https://iphylo.blogspot.com/2015/05/text-mining-for-museum-specimen.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/f13eq-bcg72","id":"313615e0-305c-4d18-ad68-ecdb6527c4d4","image":"http://lh5.ggpht.com/_Gct8lVAxKqQ/TQDKnlA2n7I/AAAAAAAAAzg/smFsn6PMkzA/photo.PNG?imgmax=800","indexed_at":1694279713,"language":"en","published_at":1321620660,"reference":[],"summary":"One
thing I''m increasingly conscious of is that I''ve a lot of demos and toy
projects hanging around and the code for most of these isn''t readily available.
So, I plan to clean these up and put them in GitHub so others can explore
the code, and reuse it if they see fit.First up is the code to create a HTML+Javascript
clone of Nature''s iPhone app, as described in an earlier post.There''s a
live version of the clone here here.","tags":["Github","Javascript","J Query
Mobile","Nature"],"title":"Nature iPhone app clone in GitHub","updated_at":1321620707,"url":"https://iphylo.blogspot.com/2011/11/one-thing-im-increasingly-conscious-of.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/z8g5k-peb09","id":"caba40a1-2a0a-429f-9c57-c163cf2e9ff8","image":"http://lh3.googleusercontent.com/-KBiVfFvubjM/VUzyDYGQuII/AAAAAAAADus/GtUQB590U5o/m13QFZi4.jpeg?imgmax=800","indexed_at":1692833025,"language":"en","published_at":1431105900,"reference":[],"summary":"@rdmpage
@BioDivLibrary @bouchoutdec Why aren''t you creating an iphylo blog what metrics
you expect to see so you will not be disappointed?\u2014 Donat Agosti (@myrmoteras)
May 1, 2015 There are no requirements for signing up. A signature is first
and foremost a statement of support for open data . Each signatory can determine
how best to make progress towards the goal. Some recommendations are included
in the declaration.","tags":["Bouchout Declaration","Open Access","Open Data"],"title":"Putting
some bite into the Bouchout Declaration","updated_at":1431106064,"url":"https://iphylo.blogspot.com/2015/05/putting-some-bite-into-bouchout.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/w3afa-cyh60","id":"920b37df-4f55-48b6-b9d2-de32ebe16506","image":"http://lh6.ggpht.com/-Bt4LB6Z1uLg/VS6Pv30YSGI/AAAAAAAADtE/1cFVOP5Uzkc/f1.png?imgmax=800","indexed_at":1692837209,"language":"en","published_at":1429114800,"reference":[],"summary":"The
six finalists for the GBIF Ebbe Nielsen Challenge have been announced by GBIF:
\u201cThe creativity and ambition displayed by the finalists is inspiring\u2019,
said Roderic Page, chair of the Challenge jury and the GBIF Science Committee,
who introduced the Challenge at GBIF\u2019s 2014 Science Symposium in October. \u201cMy
biggest hope for the Challenge was that the biodiversity community would respond
with innovative\u2014even unexpected\u2014entries,\u201d Page said.","tags":["Challenge","GBIF"],"title":"GBIF
Ebbe Nielsen Challenge finalists announced","updated_at":1429114840,"url":"https://iphylo.blogspot.com/2015/04/gbif-ebbe-nielsen-challenge-finalists.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/aane1-k2364","id":"6e877a50-f09b-4aed-9ae6-40fd5313bdf8","image":"http://lh6.ggpht.com/-wxBve_I6WWc/TnhEmYBkpKI/AAAAAAAAA_4/__ClTGzQX8Y/Unknown.gif?imgmax=800","indexed_at":1694285578,"language":"en","published_at":1316504700,"reference":[],"summary":"I''ve
been spending a lot of time recently mapping bibliographic citations for taxonomic
names to digital identifiers (such as DOIs). This is tedious work at the best
of times (despite lots of automation), but it is not helped but the somewhat
Orwellian practices of some publishers. Occasionally when an established journal
gets renamed the publisher retrospectively applies that name to the previous
journal.","tags":["Crossref","DOI","Entomologica Scandinavica","Graphviz","Insect
Systematics And Evolution"],"title":"Orwellian metadata: making journals disappear","updated_at":1316505138,"url":"https://iphylo.blogspot.com/2011/09/orwellian-metadata-making-journals.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/dzyd9-j8y33","id":"107632f5-7144-4c99-86dc-df8c6485c9df","image":"http://lh3.ggpht.com/--a2sSrAiZaM/Tm_BEaEmW1I/AAAAAAAAA_A/yn28RlwZeBU/mendeley_duplicate.png?imgmax=800","indexed_at":1694287392,"language":"en","published_at":1315946760,"reference":[],"summary":"Browsing
Mendeley I found the following record: http://www.mendeley.com/research/description-larva/.
This URL is for a paperCosta, J. M., & Santos, T. C. (2008). Description of
the larva of. Zootaxa, 99(2), 129-131which apparently has the DOI doi:10.1645/GE-2580.1.
This is strange because Zootaxa doesn''t have DOIs.","tags":["Duplication","Error","Matching","Mendeley","Merging"],"title":"Phantom
articles: why Mendeley needs to make duplication transparent","updated_at":1315947417,"url":"https://iphylo.blogspot.com/2011/09/phantom-articles-why-mendeley-needs-to.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/axeqb-q2w27","id":"69aa868f-a0f1-4b7f-8ef3-0a57079f2aff","image":null,"indexed_at":1689936287,"language":"en","published_at":1689700920,"reference":[],"summary":"To
much fanfare BiCIKL launched the \u201cBiodiversity Knowledge Hub\u201d (see
Biodiversity Knowledge Hub is online!!!). This is advertised as a \u201cgame-changer
in scientific research\u201d. The snappy video in the launch tweet claims
that the hub will it will help your research thanks to interlinked data\u2026
\u2026and responds to complex queries with the services provided\u2026 Interlinked
data, complex queries, this all sounds very impressive.","tags":[],"title":"What,
if anything, is the Biodiversity Knowledge Hub?","updated_at":1689701225,"url":"https://iphylo.blogspot.com/2023/07/what-if-anything-is-biodiversity.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/7n7jf-tv510","id":"8f95db43-956b-4d0a-91a9-7127d20c502c","image":"http://lh6.ggpht.com/-RrBlgC9Y-Tw/VMGBBigOS-I/AAAAAAAADp8/KJ4Z96fdmHc/Banza.png?imgmax=800","indexed_at":1692844091,"language":"en","published_at":1421967600,"reference":[],"summary":"For
the last few weeks I''ve been working on a little project to display phylogenies
on web-based maps such as OpenStreetMap and Google Maps. Below I''ll sketch
out the rationale, but if you''re in a hurry you can see a live demo here:
http://iphylo.org/~rpage/geojson-phylogeny-demo/, and some examples below.","tags":["Geo
JSON","Geophylogeny","Google Maps","Open Street Map"],"title":"GeoJSON and
geophylogenies","updated_at":1421967642,"url":"https://iphylo.blogspot.com/2015/01/geojson-and-geophylogenies.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/zfdfv-82093","id":"dab00071-3c53-4f2f-91ee-4b7c64bf57fa","image":null,"indexed_at":1692838883,"language":"en","published_at":1422444120,"reference":[],"summary":"Below
I sketch what I believe is a straightforward way GBIF could tackle the issue
of annotating and cleaning its data. It continues a series of posts Annotating
GBIF: some thoughts, Rethinking annotating biodiversity data, and More on
annotating biodiversity data: beyond sticky notes and wikis on this topic. Let''s
simplify things a little and state that GBIF at present is essentially an
aggregation of Darwin Core Archive files.","tags":["Annotation","DOI","GBIF","Github","Nanopublication"],"title":"Annotating
GBIF, from datasets to nanopublications","updated_at":1422445414,"url":"https://iphylo.blogspot.com/2015/01/annotating-gbif-from-datasets-to.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/qbcrs-4b509","id":"17a62f7e-89f6-46c3-a49c-ad72efcdbcb8","image":"http://lh4.ggpht.com/-xAbSv951fWk/Tm8KHo3yd8I/AAAAAAAAA-4/QksWyr18mBw/n2_w1150.png?imgmax=800","indexed_at":1694287985,"language":"en","published_at":1315899900,"reference":[],"summary":"Following
on from my previous post on BHL apps and a Twitter discussion in which I appealed
for a \"sexier\" interface for BHL (to which @elywreplied that is what BHL
Australia were trying to do), here are some further thoughts on improving
BHL''s web interface.Build a new interfaceA fun project would be to
create a BHL website clone using just the BHL API.","tags":["API","BHL","Bio
Stor","Flickr","Interface"],"title":"More BHL app ideas","updated_at":1315899936,"url":"https://iphylo.blogspot.com/2011/09/more-bhl-app-ideas.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/ywcfw-14e12","id":"5cae8c9b-b770-4cd3-a325-7ef6018d7320","image":"http://lh3.ggpht.com/-eeNrhmKzL7M/VJHL-BKdRYI/AAAAAAAADms/oVtPPYm3w08/bold.png?imgmax=800","indexed_at":1692842873,"language":"en","published_at":1418841060,"reference":[{"doi":"http://doi.org/10.1111/j.1755-0998.2012.03119.x","key":"ref1"},{"doi":"http://doi.org/10.1093/sysbio/syu028","key":"ref2"},{"doi":"http://doi.org/10.1186/1745-6150-5-47","key":"ref3"},{"doi":"http://doi.org/10.1093/sysbio/syu060","key":"ref4"},{"key":"ref5","url":"http://mitpress.mit.edu/books/vast-machine"},{"doi":"http://doi.org/0.1371/journal.pone.0068535","key":"ref6"},{"doi":"http://doi.org/10.1016/j.ympev.2013.04.034","key":"ref7"},{"doi":"http://doi.org/10.1071/is12008","key":"ref8"}],"summary":"On
a recent trip to the Natural History Museum, London, the subject of DNA barcoding
came up, and I got the clear impression that people at the NHM thought classical
DNA barcoding was pretty much irrelevant, given recent developments in sequencing
technology. For example, why sequence just COI when you can use shotgun sequencing
to get the whole mitogenome?","tags":["DNA Barcoding","Metagenomics","Vast
Machine"],"title":"Is DNA barcoding dead?","updated_at":1418841088,"url":"https://iphylo.blogspot.com/2014/12/is-dna-barcoding-dead.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/qgb4x-1te73","id":"45bd6dfc-068c-4ed1-b601-0001b08bcbf9","image":"http://4.bp.blogspot.com/_Gct8lVAxKqQ/RyOFc_vHnzI/AAAAAAAAAHs/xepS7-668OQ/s320/sun.sparcstation5.12.jpg","indexed_at":1693679585,"language":"en","published_at":1193509800,"reference":[],"summary":"No,
not taxonomy the discipline (although I''ve given a talk asking this question),
but taxonomy.zoology.gla.ac.uk, my long-running web server hosting such venerable
software projects as TreeView, NDE, and GeneTree, along with my home page.A
series of power cuts in my building while I was away finally did for my ancient
Sun Sparcstation5, running the CERN web server (yes, it''s that old).
I can remember the thrill (mixed with mild terror) of","tags":["CERN","CVS","Mac
OS X","Sun"],"title":"Taxonomy is dead, long live taxonomy","updated_at":1193518355,"url":"https://iphylo.blogspot.com/2007/10/taxonomy-is-dead-long-live-taxonomy.html"},{"archive_url":null,"authors":[{"name":"Roderic
Page","url":"https://orcid.org/0000-0002-7101-9767"}],"doi":"https://doi.org/10.59350/t4hy9-0mv62","id":"64b79d80-1e32-4e29-aeee-465a5fd26779","image":null,"indexed_at":1693680785,"language":"en","published_at":1192346580,"reference":[],"summary":"Here
is a live demo of Pygmybrowse using the Catalogue of Life classification of
animals provided by GBIF. It''s embedded in this post in an