Saturday, October 4, 2003
Human Protein Reference Database
The Human Protein Reference Database has been unveiled. Here's the paper published in Genome Research, and an accompanying press release. Neither paper nor press release mentions it, but the source code to the site (not including templates) is open source and available under the LGPL license.
Congratulations to the teams at Pandey Lab and Institute of Bioinformatics, who worked their asses off for over a year to make this happen.
Two people not co-authors on the paper, but who also contributed, are Sandeep Chandur (![[info]](http://l-stat.livejournal.com/img/userinfo.gif)
irq2), who wrote the XML parsing routines for the initial data import into Zope, and Allan Stanley (killapop), who designed the user interface.
Congratulations to the teams at Pandey Lab and Institute of Bioinformatics, who worked their asses off for over a year to make this happen.
Two people not co-authors on the paper, but who also contributed, are Sandeep Chandur (
irq2), who wrote the XML parsing routines for the initial data import into Zope, and Allan Stanley (killapop), who designed the user interface.
fus — Oct 4, 2003 4:43:57 AM — # ↩
another thing neither the paper nor the release mention, but that which should be mentioned nay highlighted, is that this is the first biological database which takes a complete object oriented approach. the design is a marvel.
manusb — Oct 4, 2003 3:22:25 PM — # ↩
Learnt that word while reading Rising Sun.
Anonymous — Oct 4, 2003 5:10:13 PM — # ↩
Hi, I'm a biology student setting my first steps in the worlds of databases (I'm currently in the proces of making a local mirror of the OMIM database).
So, could you please explain to me why a object-oriented database was better suited for this project than a relational database. One of the benefits I read about, is that there's no limit on the number of entries (i.e. proteins) or the number of characteristics that can be included in a object-oriented database, but I don't see why this shouldn't be possible in a relational datbase.
Please enligthen me,
Jeroen Van Goey
fus — Oct 5, 2003 1:39:12 AM — # ↩
hth
Kiran Jonnalagadda — Oct 5, 2003 3:32:48 AM — # ↩
In a relational database, if you want to add a new property that is NOT attached to all objects, it has to go into a separate table.
Now try creating a database where almost all properties are optional, and you will end up with a large collection of small tables that get increasingly difficult to make sense of. A hierarchical database doesn't suffer from this fragmentation (but has other problems, like when a node needs to have two parents, or needs to be moved to another parent).
An object oriented hierarchical database, which the Zope Object Database (ZODB) is, puts data and the code to manipulate the data in the same place, making source code management much easier for the programmer.
ravi — Oct 4, 2003 3:10:54 PM — # ↩