Tooled up bibliographies

I've just got around to installing the magnificient kcite plugin that Simon Cockell wrote for knowledgeblog. It's actually a really simple plugin, but it's tremedously useful. For instance, I can now cite my own papers on reality [cite source='doi']10.1371/journal.pone.0012258[/cite], function [cite source='doi']10.1186/2041-1480-1-S1-S4[/cite] or protein classification [cite source='doi']10.1093/bioinformatics/btl208[/cite] and all the metadata will be gathered and cited for me in a nice reference list at the end. Of course, I am used to the good life, and this is still all a bit clunky for me. I wanted support from my text editor. For this blog, I use a tool-chain of Emacs, asciidoc and blogpost. But for references I use reftex mode and bibtex. Now I realise that this is a pretty minorit…

Test2

Test pass::[[cite source='doi']10.1371/journal.pone.0012258[/cite]] pass::[[cite source='doi']10.1186/2041-1480-1-S1-S4[/cite]] Here is an inline citation modified doi:10.1186/2041-1480-1-S1-S4. Here is a inline pmid pmid:43242432, and here is a kurl:knowledgeblog.org http://test.com

The Problem with DOIs

This article was jointly author by Phillip Lord and Simon Cockell. Rhodopsin is a protein found in the eye, which mediates low-light-level vision. It is one of the 7-transmembrane domain proteins and is found in many organisms including human. Rhodopsin has an number of identifiers attached to it, which allow you to get additional data about the protein. For instance, the human version is identified by the string "OPSD_HUMAN" in uniprot. If you wish, you can go to http://www.uniprot.org/uniprot/OPSD_HUMAN and find additional information. Actually, this URI redirects to http://www.uniprot.org/uniprot/P08100.html. P08100 is an alternative (semantic-free) identifier for the same protein; P08100 is called the accession number and it is stable, as you can read in the user manual. If y…

An announcement

This blog has been alive now since Feb 2006. It started with a relatively uneven tone, as many blogs do, moving between the personal and the professional, the and the, erm, less trivial; the first posts were a mildly witty observation about an airport, a review of Breakfast at Tiffany's and a discussion on semantic enrichment of literature which seems as true then as now. I think that it has now reached a more even state --- it's generally moving in a more professional blog while, perhaps ironically, my profession has moved more toward blogging. It contains very little of my personal life for reasons explained earlier. I would like to beg the indulgence of my readers, both of whom know this anyway, by using my blog to announce the birth of our son, Sean Maioli Lord on 7th Dec 2010. He was …

The Status Quo farewell tour on realism

I originally wrote this as a brief comment in reply to David Osumi-Sutherlands excellent post. But, the formatting got mixed up and is unfixable there, so I posted I am posting it here. Not only do I believe in mind-independent reality, I believe that science makes claims about mind independent reality that it is reasonable to believe are true. In my experience, most scientists (certainly most biologists) believe this too. --- David Sutherland I agree. However, this has little or no bearing or relevance to whether you are a realist or not. The assumption that it does it based on an etimological fallacy --- "realism" chose a good name, this is all. Conceptualists, or people like myself who just don't care about the philosophy, but who simply find that realism is resulting in ba…

Why Not?

My last post was an attempt to drag myself out of the realism debate; unfortunately, Chris Mungall replied, and he deserves an answer. Fortunately, his comment addressed an issue that I have been meaning to post for a while, which is the use of "not", or "absent" in an ontology. I'll make a brief aside into realism, then describe the pragmatic design decisions that lie at the heart of the issue. Feel free to skip the realism bit. The realist objection "I wasn't aware of the realist objection to the not / complementOf construct." --- Chris Mungal Obviously, the standard problem with realism is that it is ill-defined, so it is, therefore hard to determine exactly what is does mean. My reading that realism objects to "not" comes from the "Beyond…

Why Realism is Wrong

Following the publication of a number of papers, Gary Merrill, Michel Dumontier and Robert Hoehndorf (also as PDF) and myself (also on PLoS One), there has been an enormous amount of discussion on what is realism in ontology building, and whether it appropriate for use in scientific ontology building. As I have documented previously, I had now left the BFO discuss mailing list, and more latter OBO discuss, as I felt that these discussions have reached a finishing point. In this post, I want to spell out clearly my reasons why I think that it is not appropriate. I want to try and avoid re-iterating the positions in my paper, and earlier postings, as well as provide a direct answer to David Sutherland who has posted why he is a realist. What is realism? Sadly, I need to start with a philosop…

The problem with institutional repositories

I don't normally use my blog to engage in conversations the way that some people do. I already spend enough time on mailing lists, so using the blog seems redundant for this. However, I will change the habit of a life-time this once, because of an interesting discussion on institutional repositories, which I have previously written about myself. To me the difficulty with institutional repositories is this. First, they are a resource. Then, some one says, this is good, everyone should do this. Then, someone else says, hey this is great, we could use this for our RAE (REF, whatever) return. Now, you have to deposit things in your IR. But people object, on various "data is mine" grounds, so perhaps they make the IR non-public. The data model gets tweaked with various additional data…

Deleted My Networking

While travelling on Elba, I suffered the misfortune of a virus attack; I don't use AV software these days, since it tends to break other things which take a long time to fix, and it's been many years since I've lost a machine to malicious software. The process, though, was quite entertaining. First, I started getting an error stating that system.exe needed .net to run properly. After a while, a Windows update happened, along with the normal malicious software removal update. This found the virus, probably killed it, then stuck up a dialog saying "Some of your files were nasty, so they need to be restored, please insert your Windows SP3 disk". Clicking "ok" said "I can't find the disk, perhaps a) you put the wrong disk in or b) your drive isn't working". Or c) …