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…
Test
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
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…
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 …
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…
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…
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…
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…
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) …