In my previous post I checked how many of the databases listed in DBcat and the NAR database issue from 1999 were still reachable. I did this as a quick way to try and gain an indication as to how databases have become extinct. This approach, as I acknowledged, had a number of limitations. Indeed, [...]
In my previous post I showed the number of biological databases in existence is growing each year. Here I wish to try and gain an insight into how many databases are now unreachable and thus have likely become extinct. Although a number of “database of databases” exist, they will only contain databases that are currently [...]
As is commonly stated, biological data is constantly increasing. However, although it is well known that the number of databases in existence is growing, it is less common to see discussions regarding this growth. The growth of biological data is frequently illustrated by showing a graph of the data being added to a database such [...]
The majority of the work discussed on this blog has looked at annotations within UniProtKB. In a nutshell, we have shown high levels of annotation reuse, which is essentially done as a matter or protocol. I’m now in the process of writing up, and have just been looking at citation information in UniProtKB. Although not [...]
Earlier today I presented our work on annotation quality at ECCB’12. This was my first time presenting outside of an internal lab seminar and it was a great experience. I was in the 525 seater Montreal auditorium at the Congress Center Basel, which was a really nice place to talk. There was a good number [...]
Just a quick post to say that our paper has now been published by Bioinformatics: “An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB”
As mentioned previously, we (Colin Gillespie, Daniel Swan, Phillip Lord and I) have recently had some of our work on annotation quality accepted at the European Conference on Computational Biology (ECCB’12). Given this, I am due to give an oral presentation at ECCB’12 in Switzerland on the 11th September (ECCB’12 Schedule). I have made this [...]
In the previous post I introduced some animated graphs that were produced to aid the analysis of Swiss-Prot and TrEMBL annotations overtime. Visual inspection of these graphs is beneficial, however the main analytical value comes from the extracted alpha values for each graph – something which I could have included. Many thanks to Colin Gillespie [...]
Carrying on from the previous post, we now wish to look at annotation maturity in sets of UniProtKB entries. We have seen that over time the quality of annotations appear to be decreasing over time, for both Swiss-Prot and TrEMBL. A reasonable explanation for this would be that annotations are constantly being added to the [...]
As we know the UniProtKB database is growing exponentially. Our prior quality analysis of whole UniProtKB versions has seen that, over time, annotations are becoming more geared towards the annotator; that is, readers now require more effort to interpret and digest the annotations than in earlier versions of UniProtKB. The exponential growth of the database [...]