Ontology Development group summary
23 May 2006
First draft of a merged document to describe the Ontology Development Group formed by merging the (ontology development activities of) the GO Editorial Office and the Annotation-Ontology Development Group.
- What is the group’s purpose?
- This group directs and implements the development of GO in keeping with Aim 1: We will maintain comprehensive, logically rigorous and biologically accurate ontologies.
- Our goal is to ensure that the Gene Ontology represents biology in a way that is useful for biologists. In particular, the GO should accurately reflect current knowledge of biological systems, and support gene product annotations — both of reference genomes and by other MODs using the GO — to advance scientific investigations and data analysis.
- What makes this group necessary and unique?
- Because ontology content is central to the GO effort, the GO project requires staff dedicated to ensuring comprehensive coverage and quality (i.e., biological accuracy and logical rigor). This group naturally includes all of the GO Editorial Office staff, as well as database curators who are actively involved in GO annotation. The members who are annotators serve as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology.
- What is the lifespan?
- This group will endure for the length of the project.
Jane Lomax (GO Editor, EBI) & David Hill (Scientific Curator, MGI, The Jackson Laboratory)
A full-time GO editor (Jane) and an experienced MOD-based GO annotator (David) jointly lead the group, helping ensure good communication between the GO Editorial Office and annotators throughout the GOC.
- What are the key deliverables of this group?
- The group establishes liaisons between our annotation staff and the GO central office. We are responsible for an open line of communication between the ontology developers and the biologists. We are available to review pertinent SourceForge requests for new biological content in the GO. When issues arise concerning biological content, we ensure that an expert biologist/annotator is available who can judge and comment on the issue. We serve as the “biologists' eyes” in the compromises that are necessary in ontology development.
- We provide large modifications to GO content and structure. We are responsible for collecting the opinions of experts and expanding and refining the GO. Currently there are three ongoing large-scale revisions/extensions to the GO:
- Immunology revision (headed by Alex Diehl): This project is under way and changes will be in place in the GO by June 15.
- Neurobiology revision (headed by David Hill, Doug Howe and Cynthia Smith): This revision will be a large expansion of the ontology in the area of central nervous system development. Drafts of the expansion are being circulated, and an interest group meeting will take place in June. The modifications to the ontology will be made by August 30.
- PAMGO revision
- We work with the software development group to be sure that the GO remains useful and comprehensible to biologists. We work with both OBO-edit group to enhance tools and the AmiGO group to enhance visualization.
- We work with other groups in the OBO foundry to coordinate efforts in ontology development between GO and other relevant biological ontologies.
- What criteria are used to set priorities?
- Priorities based on biology are set by interactions with three groups: the reference genome annotation group, the outreach group and the biological community.
- Since one of the primary foci of this funding period is the annotation of reference genomes, we work closely with Reference Genome Focus group to be sure that the ontology is sufficient for the areas of biology that are undergoing intensive annotation.
- We work with the Annotation Outreach group as a conduit for ontology development related to new genomes that are being annotated. We provide members of our group as contact persons who can discuss ontology development with emerging genome groups.
- We are the ears of the biological community. We will respond to needs of biologists as issues regarding the biological integrity of the GO arise.
- In addition to biology, content priorities can be guided by identifying areas where logical consistency can be improved. For example, a current high priority is complete is_a paths in cellular component.
- Further criteria for setting priorities may emerge as the group's work progresses.
- The GO Editorial Office staff are all members:
- Midori Harris
- Jane Lomax
- Amelia Ireland
- Jen Clark
- We have 7 confirmed members who represent reference genomes. These members are experienced gene annotators who have previously contributed valuable ideas and time to content development in the GO:
- Mus: David Hill
- E. coli (prokaryotes): Michelle Gwinn
- Dictyostelium: Pascale Gaudet
- Saccharomyces: Karen Christie
- Zebrafish: Doug Howe
- C. elegans: Kimberly Van Auken
- Drosophila: Susan Tweedie
- Arabidopsis: Tanya Berardini
- To be confirmed
- Human (UniProt): Becky Foulger
- Schizosaccharomyces: Val Wood
Susan Bromberg from RGD has agreed to serve as a contact person for mammalian issues with respect to strengths of the rat system such as neurobiology and physiology. We will also consider involving additional individuals on a shorter-term basis as needed for work on specific content areas.
- We will communicate regularly at a frequency to be determined; we'll probably start with weekly or fortnightly communication by conference call or IRC.
- Face-to-face meetings are set by ontology development needs, involving key people for the domain in question. Some meetings are formal ontology development meetings, such as the Neurobiology meeting on June 15–16, 2006.
- Ideally, we would like to set up web-chat and bulletin board capabilities as well as conference call capabilities for our group.
Metrics of success
- Our most important metrics are:
- New policies for ontology content
- Ongoing content issues resolved
- Additional metrics:
- Number of new terms added
- Number of new terms that are used for annotation once changes are in place
These metrics help ensure that areas of the ontology are continually improved, as measured by number of new terms and relationships added to the ontology in specific biological interest areas. Still other metrics may be determined.
- Weekly leaders call
- Fortnightly chat/web conference (ad hoc participant lists)
- Quarterly Ontology Development Report
- SourceForge requests to discuss ontology issues
- E-mail requests and consultations with other OBO groups
- Collaborative work:
- We work with many of the other GO groups:
- Software development group - ensure that the GO remains useful and comprehensible to biologists.
- Annotation Outreach - stay informed about new groups that plan to start annotating; make any changes that new groups will need.
- We work with the GO PIs because overall project direction influences content decisions.
- In addition to intra-GOC connections, we work with the user community (via the community advocacy group) to find expert biologists to give advice; these experts may join interest groups and can help set priorities meet biologists' needs. We thus help establish Curator Interest Groups to facilitate ontology development for specific topics (note: particularly active groups may have this sort of summary done in their own right).
- We also work with other groups in the OBO foundry to coordinate efforts in ontology development between GO and other relevant biological ontologies.
- We work with many of the other GO groups:
More links within and outside the GOC may come to light as the group matures.
- What are the key decisions?
- What areas of the ontology need development?
- We work closely with the reference genome annotation group to ensure that the ontology is “up to speed” on areas that will undergo intense annotation.
- We listen to the biological community for any constructive criticism involving biological content in the GO.
- We work with the outreach group to ensure that emerging genomes have the terms in the ontology to represent their needs. Experience has shown that since most emerging genomes use large-scale methods for annotation, many of these terms are specialized high-level terms and are limited in number.
- What tools and resources do we need to effectively perform our jobs?
- We work with the User Advocacy Group as issues arise about ontology content and representation. We provide feedback and the first-level biologist look at areas such as AmiGO enhancements etc.
- We work with the Software and Utilities Group to suggest new tools and enhancements to existing tools that make the job of ontology development easier.
- How are decisions made?
- Decisions about biological content issues are made by consensus within the group. In cases where members of the group have in-depth knowledge of a specific area of biology, this will be taken into account.
- Decisions about areas of the ontology in need of development will be made through direct contact with the Reference Genome Annotation Group and the Outreach Group.
In some cases, if issues cannot be resolved, the questions will be escalated to the GO Directors or to a Consortium meeting.
- What Is the flow of choices?
- Areas of the ontology are identified by the reference genome annotation group, the outreach group, the user community, or the ontology content group itself.
- The leaders are responsible for contacting appropriate group members for the ontology development; David Hill will ensure that annotators are well represented.
- Once a team is formed they report on both the extent and time-frame of proposed changes.
- The team of experts works to produce a proposal for modifications to the ontology.
- Team members forward a proposal to the entire working group for review of biological accuracy.
- Once approved by the group, the proposal is forwarded to the GOC for review.
- The GOC can approve the proposal
- The GOC can request a revision of the proposal
- The working group can resolve the issues
- The working group cannot resolve the issues
- The issues are forwarded to the GO Directors.
- The issues are tabled for discussion at a GOC meeting.
- Once approved by the GOC
- The GO is modified
- Requests are sent for modifications of other OBO ontologies.