David Hill and Tanya Berardini attended the Annual Meeting of The American Society for Cell Biology in San Diego in December 2009 as the second effort to attend a major meeting and use the information presented at the meeting to modify the ontology. The first successful undertaking of this style of ontology development was at The Society For Developmental Biology Meeting in 2009.
Prior to the meeting, the schedule of the meeting was reviewed and compared to the existing state of the ontology for areas that were going to be covered at the meeting. Curators decided on which talks to attend based on either a lack of terms in a branch of the ontology or areas of the ontology where they knew little work had been done. Talks about areas of the ontology that were under current scrutiny by interest groups, such as signaling, were not attended.
During the sessions there was no internet access in the meeting rooms so prior to attending the talks the current ontology was loaded into OBO-Edit and consulted as the talks progressed. New terms, or rearrangements were recorded as free-text notes. Most ontology editing was done in the meeting breaks and after the evening session had concluded. The remainder was completed after the meeting was over by skype/webex meetings. Changes were committed to the live ontology file. We did not work with a branch file.
Comments about changes were addressed immediately, sometimes within a day or two of adding terms (see SF2911084).
One complication to our strategy was the requirement that no unpublished information from the meeting be ‘broadcast’ in any way. This made it necessary for us to be certain that the information being added to the ontology was previously published. This guarantee was made by searching for published literature to back up the new information that was being added to the ontology. Although this added more effort than was initially expected, it was also useful to double-check that the information was being represented accurately. In some cases, we simply asked the speakers after their talks if their data had been published. If the data had not been published, the information was not added to the ontology.
Terms that were addressed based on this meeting were given the dbxref GOC:ascb_2009.File:ASCB 2009 terms.doc
Upon request for information about progress resulting from our attending the meeting, SourceForge items were opened to make annotators aware of the areas of the ontology on which we were working; SF2926578, SF2926570, SF2926582, SF29265659, SF2926573, SF2942461.
A total of 185 new terms were added to the ontology and 45 terms were revised based on 30 talks at the meeting. Revisions consisted of improved definitions, added synonyms, and re-placement in the graph. The meeting covered a broad range of cell biology topics, although as we had experienced at the SDB meeting, there were certain areas, such as membrane dynamics, that were emphasized due to recent developments that pushed the knowledge in those areas forward.
Areas covered: ER to Golgi vesicle-mediated transport (GO:0006888), cholesterol transport (GO:0030301), cell-cell signaling (GO:0007267), Golgi organization (GO:0007030), mitochondrial fission (GO:0000266), mitochondrial fusion (GO:0008053), sphingolipid biosynthetic process (GO:0030148), establishment or maintenance of cell polarity (GO:0007163), meiosis (GO:0007126), mitosis (GO:0007067), and various areas of RNA metabolism and localization. The following terms were added or touched based on the talks presented at this meeting.
To retrieve the terms, the following script was used, from the go-perl-0.09 package: in the directory go-perl-0.09/scripts perl obo-grep.pl -r 'GOC:ascb_2009' FILEPATH/go/ontology/editors/gene_ontology_write.obo
As with The Society For Developmental Biology meeting, we found that attending the ASCB meeting was a good value for ontology development. First, it permitted ontology curators to learn about the current status of a wide area of the cell biology discipline and to ensure that the ontology reflected the views of bench-scientists working in the field. The total cost of attending the meeting for 2 curators was $3206 and a total of 230 terms were added or modified in the ontology. This gives a final cost of approximately $14 per term. As with the SDB meeting, we found this strategy to be a cost-effective way to achieve ontology development.
In addition to the tangible benefits of ontology modification, this strategy also benefits GOC ontology developers by keeping us immersed in the experimental science that we are trying to represent in the ontology. It ensures that we are ‘talking the talk’ and ‘thinking the thoughts’ that are consistent with the way that experts in the field are treating the science. Attending these types of meetings also allows us to see how GO resources are used by research biologists. It is encouraging to hear presentations that have used GO successfully for data analysis and it is helpful to converse with the researchers who use the resource to learn what they like about GO.
Our attendance at this meeting confirms that with proper background preparation and knowledge, ontology curators can successfully develop GO using a ‘real time’ strategy in a cost-effective manner.