DataOnTools #6: omicX features

With more than 29,000 entities, omicX is the largest collection of bioinformatics tools. Our classification system allows to easily find and identify the tools you need. We conclude our series by providing some data analysis on the omicX collection.

Tool categorization system


Software tools and database are classified in one main category among transcriptomics, genomics, phenomics, metabolomics, proteomics and epigenomics. Then, they are labelled in one or more of the 2,000 subcategories. To explore the categories, check our interactive figure (Figure 1, available online).


OMICtools categories ontology comics fields
Figure 1. Overview of omicX categories


Obsolescence in bioinformatics tools


Tools are developed continuously, and usually hosted on institution servers and corporate websites. Eventually, their URLs will not be maintained and the tool will become inaccessible, obsolete.


omicX scans tools URLs every day so that you can know if a tool is really available or not. Figure 2 shows the proportion of online and offline tools according by their publication date, as of December 2017. Interestingly, the proportion of tools that are offline in 2017 is the highest for those developed in 2005 and around this year. Older tools are not necessarily less available than recent tools.


obsolescence tool
Figure 2. Tool persistence. Tools referenced in the omicX database are pinged daily to evaluate their responsiveness. If URLs are not responding, the tool is marked as “obsolete”. The percentage of online and offline tools as of March 6, 2018 is represented for each publication year.


Redundancy in tools functions


 Since a given tool can be used for more than one technology or analysis step, we extracted the number of duplications for each tool, that is the number of applications, analysis step, or function associated with a tool. The vast majority of tools in our database (82%) are assigned to one application, while 18% of tools are assigned to two or more applications (Figure 3).


duplication tools omictools
Figure 3. Number of categories by tools. Distribution of the number of tool used for only one application (yellow) or more than one application (duplicated, blue).

This closes our series on bioinformatics tools. We hope you enjoyed our statistics, and we will provide more in the future so be sure to bookmark our blog to get the latest information.