Main Page
Welcome to the Sequence Ontology Wiki
This wiki is provided as a tool for the community working with SO. It is our ambition to provide community based forum for ontology development and documentation. These pages provide both community driven and automatically generated content about the Sequence Ontology.
Search for SO terms
Search for a SO term using the search box to the left.
Browse SO terms
Use the miSO Ontology Browser to navigate the ontology and then link to the wiki page for more details about a given term.
Browse SO terms in different categories:
Contribute to SO
The SO wiki is a tool for the community to learn and and contribute to SO. Anyone can read the SO wiki. Registered users can contribute to the wiki.
- Documentation: Add to the automatically generated documentation of terms by providing information about how your group is using particular terms.
- Open up discussion about the terminology, and link to the relevant SO tracker item.
- Help us to fix errors in the ontology by bringing our attention to problems.
Current Collaborations
List of current collaborative projects for development of SO terms:
If SO does not have the term you are looking for
Term requests. Anyone can add a term request to the SO tracker on sourceforge. Please include the name of the term you need in the title, and give as much extra information as possible in the body of the text:
- A definition in the form "An A is a B that C's"
- The term you think is best suited to be the is_a parent
- One or more cross references such as pubmed ids etc
- synonyms
It is also helpful to log into to sourceforge so that when the request gets updated, or we need more info, the message will get to you. If you don't want to do this, please email the SO developers <song-devel@lists.sourceforge.net> with your request so we can discuss it if we need to.
Sequence Ontology based file formats
GFF3 Documentation
- GFF3 documentation
- GFF3 best practices - A collection of tips for how to handle tricky situations with GFF3
- GFF3 Developement
GVF Documentation
SO tool documentation
- SOBA - Sequence Ontology Bioinformatics Analysis
- miSO - Ontology Browser
- OBOB - Open Biomedical Ontology Browser
- release note generator
- annotation format converter
SO editor info
Sequence Ontology Molecules project
- description of SOM
- browse SOM
Auto-generated content
We provide nightly updates on the ontology development. We update from the most recent CVS revision, provide graphics showing the relationships including the genus and differentiae for cross product terms, and we provide an edit history for each term.
SO wiki membership
Anyone can read SO wiki. There are however, some things that only registered users can do:
- Edit the content of a wiki page and create new pages.
- Create new user accounts.
- Create your own custom page.
- Send messages to other users.
Become a registered user
Any registered user can set up a new account for a colleague. Or just send us an email keilbeck@genetics.utah.edu to tell us a bit about who you are, and we'll set up an account for you. Be sure to send us your preferred login name.
Create a registered user account
If you are already registered and logged in, you can create an account for new users.
Credits
A special thank you to Jim Hu from Texas A and M, who let us copy the basics from the GO-nuts wiki, and spent a day in Salt Lake configuring it.
