GFF3 Working Group

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Contents

Overview

GFF3 is a text-based file format for representing genomic sequence feature annotations in a manner that balances human and computer readability. GFF3 utilizes the Sequence Ontology to constrain the terms used to type features as well as the relationships between those features. Most model organism annotations are available in GFF3 format and many genome annotation tools and pipelines produce output in GFF3 format. GFF3 has remained quite stable over the last 8 years even in the face of tremendous change in the field of genomics and annotation and yet regular discussions on the so-devel mailing list indicate that there is still occasional need for clarification and update to the GFF3 specification. The GFF3 working group serves to bring together active members of the genome annotation community to consider, discuss and recommend clarifications and updates to the GFF3 specification as needed.

Membership

Members of the GFF3 Working Group are chosen by Sequence Ontology developers and/or by an existing GFF3 Working Group from those actively participating in the list-serve discussions and from members of the annotation/ontology community with a working knowledge of GFF3. The Working Group is formed on an ad hoc basis and dissolved either by vote of the Working Group or after approximately 12 months of membership. The working group must have at least 7 and no more than 12 members to operate. See below for a list of current Working Group members. If you would like to serve on the working group or would like to suggest another person, please let the Sequence Ontology developers know by e-mail or on the so-devel mailing list.

Meetings

Meetings will be scheduled by Sequence Ontology developers and/or the existing GFF3 Working Group. The Working Group will typically meet via web conference 2-3 times a year, but may meet more frequently on occasion if the need arises. See below for meeting schedule, current agenda and minutes from previous meetings.

Purpose of the GFF3 Working Group

Because GFF3 has proven to be a highly successful and stable specification, changes to the specification will be limited to clarification and minor updates that improve the useability of the specification. A key purpose of the Working Group is to assure that approved changes are backwards-compatible with existing tools and annotation sets. Fundamental changes to the underlying structure of the specification are not within the scope of the working group's purview. If the Working Group feels that backwards-incompatible changes are needed to the specification, they should submit a 'Request for Comments' proposal of the changes and plans for mitigating the impact of the changes to the Sequence Ontology community via the mailing list and allow the next GFF3 Working Group to consider the changes.

Approval of Changes to the GFF3 Specification

Because the GFF3 format is in wide use by a diverse array of genome databases and bioinformatics tools, approval of changes to the GFF3 specification by the GFF3 Working Group will require a 5/7 majority vote with a minimum of 5 members voting.

Meeting and Membership Details

Current Members

  • Robert Buels - JBrowse
  • Scott Cain - GMOD
  • John Crow - National Center for Genome Resources
  • Karen Eilbeck - Sequence Ontology
  • Chris Fields - BioPerl
  • Ed Griffiths - Wellcome Trust Sanger Inst/AceDB
  • Don Gilbert - FlyBase, FleaBase, Daphnia, IUBio Archive of Biology
  • Carson Holt - Maker
  • Jim Hu - Ecoli wiki/Ecoli Hub
  • Barry Moore - Sequence Ontology, Maker
  • Terence Murphy - NCBI RefSeq
  • Lincoln Stein - GMOD, GBrowse

Next GFF3 Working Group Meeting

Past GFF3 Working Group Meetings

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