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.

How to download the Sequence Ontology

Revisions to the ontology are saved to an SVN repository. [1] on Sourceforge.

The files in this repository are automatically generated using the OORT tool [2] from the edit file (so-xp.obo). OORT saves both OBO and OWL versions of the ontology. This replaces the previous CVS versioning system [3]. The names of the saved files have changed between repositories. The following is a mapping:

CVS -> SVN
so-xp.obo ->  so-xp.obo
sofa.obo -> subsets/SOFA.obo
so.obo -> so-xp-simple.obo

The files in CVS are being updated from SVN temporarily to maintain software links.Other files will be added to the SVN repository as work progresses.

Browse SO terms

Use the [4] to navigate the ontology and then link to the wiki page for more details about a given term.

Browse SO terms in different categories:

• SOFA subset
• Biosapiens subset

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 Term Developments

The SO team has several projects underway to improve the content of the ontology. These projects are guided by small working groups.

• Repeats and Mobile Elements
• Prokaryotic Features
• Regulatory Regions
• BFO interoperability
• Terms to describe variation

Current Collaborations

List of current collaborative projects for development of SO terms:

• Synthetic Biology
• dbVar
• Ensembl

If SO does not have the term you are looking for

How to suggest a new term for the ontology: Look for existing terms miso, remembering to check synonyms. If you do not find a match, go to the SO tracker and browse the existing requests in case it has already been suggested. If so, add your comments to support it. If not, create a new request 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

Make the title of the term request informative to allow easy browsing of the request items. When you submit the request, it is sent to the SO developers. We may ask you for more information about the term, and sometimes will send it out to the developers mailing list to solicit comment from the community. We aim to have the request finalized and incorporated in SO within a week or two. 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. We encourage contributors to use the term tracker rather than email the SO developers list directly with term requests. The term tracker enables us to capture statistics on how many requests we get and how quickly we deal with them.

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
• GFF3 Working Group
• GFF3 Validation Tools

GVF Documentation

• GVF Description
• GVF Examples
• GVF Community Supported Attributes
• Using Phenotype Ontologies in GVF
• GVF Working Group

SO documentation

• SO Tool Documentation
• SO papers
• SO presentations
• Tutorials

SO editor info

• Saving SO files from OBO Edit

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 SVN 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.