Biological database PublicHouse visualized with MySQL Workbench

"PublicHouse is a publicly queryable set of biological databases constructed using the BioWarehouse biological database warehousing system." In other words it is a project, merging all kinds of biologically related databases into one central relational database which encompasses tens of millions of entries.


The project was initiated and maintained by SRI's Artificial Intelligence Center, which is known best for its DARPA related projects. SRI, or the Stanford Research Institute is one of the world's largest contract research institutes.


Publichouse can easily complete at least one quarter of one's data mining 'curriculum'. This is based on a very rough estimate of the time publichouse is saving me for one of my research projects. Whilst their SQL server is indeed quite fast -though 'demanded' at times, to put it mildly- their user frontend and webserver has seen better days. On the menu of web-interfaces is phpMyAdmin, which is quite wasteful with application-resources to begin with.

Fig 1.a showing an excerpt (ca ~8%) of the relational database tables of publichouse

As such a relationship map is quite useful, especially with the option of quickly navigating to the table of interest by searching for a keyword within the browser. This option becomes possible when viewing the map as an SVG (uncompressed 5MB).




Click here to view the Database as png (1.9MB)
Click here to download/view the Database as svg.gz (1.9MB)
Click here to download/view the Database as svg (5MB)
Click here to download/view the Database as pdf with captions (2MB)
Click here to download/view the Database as pdf without captions (2MB)


Note: There is a minor bug in MySQL workbench. When changing the model settings, you will have to change the Model>Relationship Notation in order to 'commit' the change, and then revert back to your Relationship Notation of choice.


Crow'S foot's Notation is used:

Fig 1.b overview of the most important relationship symbols in crow's foot notation of (RDB) tables. (Adapted from  http://ironbark.bendigo.latrobe.edu.au/subjects/IS/sem12007 )

Links:

• MySQL
• biocyc,...cyc (powered by biowarehouse)
• SRI
• biowarehouse