Sequence Ontology Workshop
On Plasmids, Phages, Transposons and Other Mobile Elements.
September 18-19th, 2006
Post Workshop Resources
- Post workshop breakdown - Karen Eilbeck
- MGE tutorial - Anne Summers
- Phages - Arriane Toussant
- RNA Editing - Jessica Kissinger
- Updated Ontology
Aim of this workshop
The aim of this workshop is to better represent plasmids, phages, transposons and other mobile elements in the Sequence Ontology. We will define what the key concepts are, what they are composed of and how they relate to other biological sequences. We will classify the terms according to different aspects:
- Kinds of natural mobile elements,
- Parts of mobile elements,
- Uses of mobile elements.
This will allow sequences to be better annotated in the biological setting (e.g. a plasmid belonging to a prokaryote), and in the reagent setting (e.g. a plasmid used as a reagent in an experiment). The ontology will be edited as we progress through the workshop sessions and the resulting decisions will be written up in a document and presented on the SO webpage. At the end of the workshop we aim to have a new and improved Sequence Ontology.
Each session will begin with a brief outline of where are with the ontology development for that particular issue. We will then engage in discussion with the domain experts to elucidate the key terms and define where they belong in the taxonomy and what relationships they have to other terms. Attendees will each have the opportunity to voice their views and drive the ontology development. As the discussion progresses we will edit the ontology to reflect the consensus opinion.
The workshop will be held over a day and a half in Hinxton, right after the Genome Informatics meeting. There will be 6 sessions to address the issues and build the ontology:
- Session 1: Overview of the aims and practices of the Sequence Ontology. We will present a short introduction to the Sequence Ontology. We will describe the present architecture and organization, including the types of terms and relationships. We will discuss the scope of the ontology, who is using it and how it is used.
- Session 2: Plasmids. We aim to identify the types of plasmid. How do these terms relate to other terms in the ontology.
- Session 3: Constructs. How should we define a construct? A construct is a region of sequence. What can it be composed of, and what can it be a part of?
- Session 4: Phages. We aim to identify the key terms relating to the sequence of phages.
- Session 5: Transposons. The SO already contains some terms for the annotation of transposable_elements. How can we make this better?
- Session 6: General feedback and comments.
- Karen Eilbeck, University of Utah
- Suzanna Lewis, Lawrence Berkerley National Labs
- Michael Ashburner, University of Cambridge
To attend this workshop, please email Karen Eilbeck.
Workshop Location and Travel Details
Cambridge is on the main line from London King's Cross. Whittlesford, Great Chesterford and Audley End stations are on the line from London Liverpool Street to Cambridge. The journey time from London is under an hour. Please note that Whittlesford and Great Chesterford stations do not have a taxi rank or telephone. Please use either Cambridge or Audley End stations if a taxi has not been pre-booked.
From airports Stanstead (~ 1 hour), LHR (~2.5 hours) and Gatwick (~4 hours) to Cambridge (Drummer Street) National Express
From Cambridge to Hinxton local bus #32
Local taxi firms:
- Phil's Taxi Services - Tel: 01223 521918
- Mid Anglia - Tel: 01223 836000
- Panther Taxis - Tel: 01223 715715
- Walden cabs 01799 500500 or 01799 599599
- Abel Cars - 01799 513313
- A&M Carriages (Airport Specialist) - Tel: 01223 513703
- MasterCab (Airport Specialist) - Tel: 01223 566654
- Crocus Cars - 01799 525511
- Camcab 01223 704704