Michael Bell

Ph.D. Students Blog

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Category: Uncategorized

Annotation maturity: Comparison of annotations in new and old sets of UniProtKB entries.

3 February, 2012 (14:57) | Uncategorized | By: mj_bell

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 […]

Annotation maturity: Average entry age within UniProtKB

26 January, 2012 (11:04) | Uncategorized | By: mj_bell

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 […]

Most frequently occurring sentences in UniProtKB and their propagation through the Web

4 November, 2011 (16:16) | Sentence reuse, Uncategorized | By: mj_bell

As already established, sentence reuse is common within UniProtKB. Obviously, some sentences will have higher reuse than others, giving an indication as to their information content. Below we show the top 10 sentences for the first versions of Swiss-Prot and TrEMBL, and also for Version 15 of UniProtKB/TrEMBL and UniProtKB/Swiss-Prot. Top 10 sentences for Swiss-Prot […]

Producing web-based dynamic graphs

5 August, 2011 (13:05) | Sentence reuse, Uncategorized, Website | By: mj_bell

As part of my work on sentence reuse I have been investigating ways to visualise various sets of data on my website. An obvious requirement of this is that the graphs must be developed dynamically; the resulting graph depending on a users query. We also have to account for various types of data, not just […]

Levels of sentence reuse in UniProtKB

26 July, 2011 (12:35) | Sentence reuse, Uncategorized | By: mj_bell

As is frequently highlighted, data being added to biological databases is ever increasing; typically at an exponential rate. This is true for the number of entries added over time to both UniProtKB/Swiss-Prot and UniProtKB/TrEMBL, as illustrated below:   UniProtKB offer a number of detailed statistics for each release of Swiss-Prot and TrEMBL, including the total […]