Biodiversity Informatics is the poor, country cousin of Bioinformatics. Where bioinformatics is concerned with the computational aspects of genes and their expression within organisms (usually in the lab) biodiversity informatics is concerned with how we handle data about the occurrence and identity of whole organism out there in the wild or dead in collections of voucher specimens.
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It was 20 years ago today, not that Sgt Pepper taught the band to play but that I submitted my PhD thesis. Of course that is not what they are talking about in the papers. They are all talking about J.K. Rowling and a mildly successful tome Harry Potter and the Philosopher’s Stone that just happened…
Read More Harry Potter and the Hairy Rhodies
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Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects
Read More Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects
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How Green Is Edinburgh Really?
Read More How Green Is Edinburgh Really?
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Automated sampling of perceived naturalness across Edinburgh
Read More Automated sampling of perceived naturalness across Edinburgh
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Today I gave my three minute presentation in the FameLab Scottish Final at the National Museum of Scotland in Edinburgh having got through the Edinburgh heat. Needless to say I didn’t win. But reflecting on the whole experience I think it was very worthwhile. Even after treating myself to sticky cake and a book from…
Read More A future without species: The acme of my FameLab career
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These are just some handy links for me to present at a CETAF Information Science and Technology Committee meeting in Geneva, October 2015. What RBGE publishes Example Edinburgh URI: http://data.rbge.org.uk/herb/E00393164 Leads to 303 redirect with content negotiation: Humans get: Catalogue Page Machines get: RDF page Our RDF also contains a link to an image resource which…
Read More Handy Links for Geneva MeetingJust posted this about the apps I’m working on. First Audio Leaflet: Dawyck Scottish Trees Trail This is also a test of the new WordPress oembed feature.
Read More First Audio Leaflet: Dawyck Scottish Trees Trail » Botanics StoriesI have been on core staff at the Royal Botanic Garden Edinburgh for a year now and, as part of my role there, have established a WordPress blog for the institution. This will act as a combined blogging platform for everyone associated with the organisation as well as a more general tool for gathering information…
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A friend just sent this photo of me collecting Rhododendrons in SW China in 1994 – as good as twenty years ago. Looking in the mirror I think I need to loose some weight. Thin suited me better!
Read More Twenty Years And At Least Twenty Pounds Lighter!
Phytotaxa 73: 17–30 (2012)
Well maybe it won’t rock science to its foundations but it is nice to have our paper finally published after delays with the proofs. Hyam, R.D., Drinkwater, R.E. & Harris, D.J. Stable citations for herbarium specimens on the internet: an illustration from a taxonomic revision of Duboscia (Malvaceae) Phytotaxa 73: 17–30 (2012). A taxonomic revision…
Read More A Great Day For Science?I am busy writing a summary of our information resources at RBGE and as part of this I am asking people to list what the high level ‘uses’ of their databases are. I am just after a power point or two worth of information. Most of these databases are catalogues of physical objects – they…
Read More General Functions of a Collections Management SystemI have been seeing DataCite.org mentioned quite a lot so I thought I’d take a look at what they were up to. They have an OAI-PMH provider so you can simply go to the List Records page and see how many records they have. Try it for yourself now. At the bottom of the page…
Read More DataCite.org AnalysisWhilst I have been working on digitizing the Rhododendron monographs I have also been providing some technical help for Stuart Lindsay who is producing a series of fact sheets for the Ferns of Thailand. This has helped crystallize my thoughts regarding monographs and how we migrate them into the digital age. This post is a…
Read More Hierarchies Make Monographs Obsolete. Fact Sheets Are The Future.I’ve had my head down work wise for the past few weeks trying to get the Rhododendron monograph markup finished. I now have a little database with some 821 species accounts in it plus a few hundred images – mainly of herbarium specimens. The workflow has been quiet simple but very time consuming. Text is…
Read More Square Peg Into A Round Hole?I have long been excited about HTML5 having access to a geolocation data. It should make it possible to build a whole range of applications for phones and other devices that are cross platform but make use of the users location. Unfortunately reality bites when you try and actually build an application based on the…
Read More HTML5 Geolocation Data SucksThis post deals with the semantics of extraction of data from the Rhododendron monographs. Another post will deal with the technicalities of the actual extraction. The image above shows a species description entry. It was chosen as being a small and simple example for illustrative purposes. I have marked up the bits I am interested…
Read More Extracting Data From the Rhododendron Monographs
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This is a sideline to my working on the Edinburgh Rhododendron monographs. The monographs often quote references to illustrations (icons) of species. This is useful as we know that these are illustrations that have been determined by the author of the account and are therefore “correctly” determined. What a shame we only have an abbreviated…
Read More Links To All Curtis Botanical Magazine Illustrations in BHLThe first two parts of the monograph to be looked at were published in Notes from the Royal Botanic Garden Edinburgh – the house journal of the gardens until 1990. Cullen, J. (1980) Revision of Rhododendron. I. subgenus Rhododendron sections Rhododendron and Pogonanthum. Notes from the Royal Botanic Garden Edinburgh. 39:1-207. Chamberlain, D.F. (1982) A…
Read More Rhodo Monographs – Clean Up 1The Royal Botanic Garden Edinburgh has a history of research into the genus Rhododendron stretching back over 100 years. The legacy of this work is a herbarium that contains many type specimens, an amazing living collection and a set of monographs that cover the whole genus. My contribution back in the 1990’s was via my…
Read More EOL Rhododendron Monographs – Getting StartedFollowing on from my previous post, European Natural History Collections – What’s Missing, it is simple to create a ranked list of countries and an estimate of the number of specimen records they have in GBIF. Countries with a score of zero don’t appear in the list. Country Specimens Spain 2,277,428 France 2,081,208 United Kingdom…
Read More Digitisation of European Collections By CountryI am working on improving the metadata on European natural history collections as part of the Synthesys project. In an earlier post (Big Collections First) I did an analysis of the data in the Biodiversity Collections Index. I am now building a more detailed list of those large collections (the ones believed to contain more…
Read More European Natural History Collections – What’s Missing?
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I’ve been slow to blog on my day job recently. Sometimes the dead ends are so embarrassing they are better not shared. One thing worth sharing is a report I did for Synthesys on improving the quality of metadata on Eurorpean biodiversity collections. It includes analysis of the data in the Biodiversity Collections Index and…
Read More Big Collections FirstLast year I did some work on a prototype system called speciesindex.org but have just taken it down and abandoned the idea. You may have reached this post via the speciesindex.org domain as it will probably resolve to here until I use it for something else. Here is how speciesindex.org was described on its one…
Read More SpeciesIndex.org – an impractical, practical solutionI am not sure how to say this. Either: I just had my first Nature Precedings paper published. I just published my first paper on Nature Precedings. The distinction is a big one. Saying I had a paper published implies the blessings of my peers. This is more like vanity publishing or even ‘stupid’ vanity…
Read More Failing To Use OWL To Merge Occurrence OntologiesThese are some figures I culled from Arthur Chapman’s excellent Numbers of Living Species in Australia and the World. The numbers speak for themselves really. Taxon # Known # Estimated % known # To Do % of Problem Chordates 64,788 80,500 80.48 15,712 0.17 Invertebrates 1,359,365 6,755,830 20.12 5,396,465 57.16 Plants (excl. Algae) 297,857 390,800…
Read More Size Of The Biodiversity ProblemI just completed my first weekend on the MSc in Mindfulness Based Approaches at Bangor University. It was a wonderful three days. I enjoyed communing with like minded people and learnt a great deal – notably some of the major differences between psychology research and taxonomy. In response to one of my questions the lecturer…
Read More Biological Diversity & Motivational DiversityJust back from TDWG2010 where I gave a talk on the use of standards in PESI and the prospect for stable identifiers for taxa. The take home message was that if we bind the identifiers to nomenclature then the identifiers will not be stable. You can see the presentation as a PDF here: PESI Standards…
Read More PESI – Standards and GUIDs at TDWG2010I was just putting my talk together for TDWG2010 and I needed a well known European species with restricted range to make a point about distribution maps. I chose Edelweiss as the name alway makes me want to break into song – plus it as a limited distribution but is in more than one country.…
Read More Edelweiss – the nomenclatural smoking gun?I have been around and around this thing over the past few years and it all comes down to a simple use-case. I thought I would present it graphically here: David is a decision maker. He wants to use data from two studies, Helen 2002 and Harry 1998. Is it safe for him to combine…
Read More Taxonomy Primal Use-CaseI’m looking to do some work on Rhododendron again and so have had to dig out the old digital copy of my PhD thesis. I have mangled the MS Word files together using OpenOffice derivative NeoOffice. For the record here is a PDF version of it. Molecular and Conventional Data Sets and the Systematics of…
Read More My Rhododendron Hymenanthes Thesis