Bilgisayar ve Bilişim BilimleriİngilizceBlogger

iPhylo

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.
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BHLLibraryMuseumNHMPresentationBilgisayar ve Bilişim Bilimleriİngilizce
Yayınlandı

Vince Smith has produced a nice flyer for my forthcoming talk at The Natural History Museum on March 17th (11-12). It will be a busy day as I'm also talking at the British Library in the evening (6pm - 8:30pm), for which Sarah Kemmitt has produced a flyer, and set up a discussion forum on Nature Network. With all this effort going into the artwork, I'd better actually come up with something useful to say.

GUIDsSemantic WebTaxonomyWikiBilgisayar ve Bilişim Bilimleriİngilizce
Yayınlandı

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.

OTUPhylogenyWikiBilgisayar ve Bilişim Bilimleriİngilizce
Yayınlandı

Another issue I'm trying to get my head around is how to deal with labels in phylogenies. These can be any number of things, such as GenBank sequences, specimen codes, taxon names, abbreviations of taxon names, laboratory codes, etc. Here's my quick attempt to model these: This sketches various levels of indirection to go from a label in a tree to a taxon name.

HostModellingParasiteTaxonomic ConceptWikiBilgisayar ve Bilişim Bilimleriİngilizce
Yayınlandı

I rather skirted around the notion of "taxonomic concepts" in the previous post, partly because it's easy to end up with trying to have a concept for each utterance every made by a taxonomist, and that doesn't seem, er, scalable. So, I have a more limited view of a taxonomic concept, namely a name attached to some data.

ClassificationDesignModellingTaxonomyWikiBilgisayar ve Bilişim Bilimleriİngilizce
Yayınlandı

Modelling taxa is a bit trickier. I've sketched my ideas for distinguishing name strings and taxonomic names earlier. That's the easy stuff. What about "taxonomic concepts" and "OTUs"? As a first pass, I'm looking at linking taxon names to classifications via GUIDs.

DesignModellingWikiBilgisayar ve Bilişim Bilimleriİngilizce
Yayınlandı

Time to make some notes. I've been playing with using Sematic Mediawiki to create a database of taxonomic names, literature, specimens, sequences, and phylogenies. One challenge is to come up with simple ways to model these entities, in a way that makes both data entry simple and querying as simple as possible. Some things are straightforward. For example, a publication can be modelled like this: OK, I've ignored the attributes.

BBCCreative CommonsPhylogenyTree Of LifeVisualisationBilgisayar ve Bilişim Bilimleriİngilizce
Yayınlandı

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.

DarwinEvolDirRSSTwitterBilgisayar ve Bilişim Bilimleriİngilizce
Yayınlandı

Well, not Darwin himself, exactly. The Evolution Directory (better known as "EvolDir") is a mailing list run by Brian Golding at McMaster University, Ontario. It's widely used by evolutionary biologists to post announcements about jobs, courses, conferences, software, and other topics of interest to the community.

"author Names""web Service"BibliometricsBioguidBilgisayar ve Bilişim Bilimleriİngilizce
Yayınlandı

One problem I've encountered in building a bibliographic database is the different ways author names are written. For example, for papers I've authored my name may be written as "Roderic D. M. Page" or "R. D. M. Page". Googling about this problem I came across Dror Feitelson's paper On identifying name equivalences in digital libraries.

MediawikiScratchpadsBilgisayar ve Bilişim Bilimleriİngilizce
Yayınlandı

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.