About My Biological Network
Google gears is an open source browser extension that enables web applications to provide offline functionality. The data are stored locally in a fully-searchable relational database using the sqlite engine.
My Biological Network is a tool I created as a test to play with Google gears: it is used to build a network of protein-protein interactions. It uses Google Gears to record your entries on the local disk, so Gears needs to be installed on your computer.
Open the tab Organism: add one or more organism. (Homo Sapiens already inserted by default)
Open the tab Protein: add one or more protein.
Open the tab Paper: add one or more article that will be used as an evidence for an interaction.
Open the tab Technology: add one or more technology that was used to characterize an interaction.
Open the tab Component: add one or more cellular component using Gene Ontology (GO:0005575 \"cellular component\" was inserted by default)
Open the tab Interaction:
- Name and describe this interaction
- Select one or more protein and/or one or more previously defined proteic complex. You Cannot describe self interactions with this tool.
-
- (optional) choose one or more paper/technology/component...
Open the
RDF table: I choose to display the content of the database using
RDF. Such format can then be validated and visualized using the
W3C RDF validator, or transformed using
XSLT, etc.... I also used the
life science identifier (LSID) as an URI for my resources.
On my computer, the database is stored in $HOME/.mozilla/firefox/<profile-id>/Google Gears for Firefox/<host>/mynetwork#database. The database can be manualy accessed using sqlite3:
sqlite3 mynetwork#database
SQLite version 3.4.0
Enter '.help' for instructions
sqlite> .tables
component interactionhash paper technology
interaction organism prote
sqlite> .schema organism
CREATE TABLE organism(id integer primary key ,name varchar(50) not null unique);
sqlite> select * from organism;
9606|Homo Sapiens
sqlite>