Biocurator meeting minutes
Sept. 20-21, 2004
Hosted by ZFIN, University of Oregon, Eugene
Meeting Moderator and Minutes Author: Doug Howe, ZFIN

This two day meeting placed an emphasis on phenotype curation, but also had talks on gene expression, ontologies, and tools. A list of participants can be found at the end of these minutes. The presentations, agenda, and these minutes will eventually be available at biocurator.org.

Aside from the presentations, there were four main discussion topics at the meeting. Resulting action items can be found at the end.

I) Should the biocurators make an effort to organize into a professional society?

1. The response to this question was 'YES'.
2. Sue Rhee sent a post to the biocurator email list which was handed out to all participants. In this email Sue indicated that Mark Johnston (GSA) and Larry Hunt (ISCB) both suggested establishing an international meeting that can grow in size as the first step towards forming a biocurator society. There was a favorable response from the group towards following up with Mark Johnston and GSA on organizing an international biocurator meeting with broader interest than the current biocurator meetings. Perhaps the biocurator email list can be used to find people who want to help put such an event together. The only issue that was raised with associating with GSA was with how this would be accepted by curators/groups that do not focus centrally on genes/proteins such as metabolic pathway groups, who were not represented at the meeting. Also, the point was made that an effort will be needed to include curators from industry. One resulting action item is below.
3. The biocurator.org website and email list has been down for several days due to a hack. Will the biocurator.org website and email list be coming back? Will it be maintained? Is the current administrator of these services willing to support their use as the biocurators organize more formally? Both the website and the email list will be instrumental in organizing the activities of the curation community. One resulting action item is below.

II) Can the MODs work together to get better access to figures in journals to support their phenotype and expression curation efforts?
MODs should compare notes on what journals they have access to in an effort to get maximum access for all MODs. These notes can be used to begin organizing a unified effort by all interested MODs to lobby journals for access permission. One resulting action item is below.

III) Does the phenotype annotation effort need more infrastructure and organization to move forward?

1. All parties interested in phenotype annotation should be subscribed to the phenotype email list at lists.sourceforge.net/lists/listinfo/obo-phenotype
2. For the time being, the group is happy with the level of organization and communication that can be achieved on the email list and did not think further infrastructure such as a dedicated website or staff (ala GO) was needed at this time.
3. The organization of shared PATO files was not clear to meeting participants. Are PATO files currently being stored centrally in a shared access CVS anywhere? As more groups think about using PATO, such a system will become important. There is a PATO attribute_and_value.ontology file available through the sourceforge obo site, but this file appears to have been last updated almost 1 year ago. As development of PATO files proceeds, standards for how shared files will be accessed, modified and stored will need to be established. Perhaps Michael Ashburner will have a comment on this with respect to the PATO file currently available on sourceforge.

IV) Can any progress be made toward promoting a database section in journals?
Interest was expressed in trying to promote a "database" section in journals. The idea outlined by Mary Polacco was to ask journals to require authors to include certain items in a predetermined format in their publication. These items might include such things as gene symbols (inherently unstable), nucleotide accessions, and perhaps MOD object identifiers (stable). The hope is that this would greatly facilitate curation efforts by MODs with limited resources, and encourage researchers to do some of the curation themselves.

The group's response to the proposal was highly mixed. Confidentiality issues were discussed as being a real hindrance in some cases. Several groups indicated that even getting journals to require that authors confirm their nomenclature with the appropriate MOD before publication had been impossible in the past. Several groups also felt that allowing authors to include GO annotation or phenotype annotation would be a big mistake. Further discussion revealed many stumbling blocks to generating a cohesive proposal for a "database" section in journals. One organizational action item resulted and is listed below.

Action items:

Participants:

Name	Organization
Martha Arnaud	Candida Genome Database
Petra Fey	dictyBase
Gillian Millburn	FlyBase
Andy Schroeder	FlyBase
Junjian Ni	Gramene
Marc Colosimo	Mitre Corp.
Cynthia Smith	MGI
Heather Hood	OHSU
Rajni Nigam	RGD
Mary Shimoyama	RGD
Charles Wang	RGD
Rose Oughtred	SGD-Princeton
Maria Costanzo	SGD-Stanford
Beth Skwarecki	Solanaceae Genomics Network
Katica Ilic	TAIR
Victoria Carollo	USDA-ARS
Mary Polacco	USDA-ARS –MaizeGDB
Wen Chen	Wormbase
Andrei Petcherski	Wormbase
David Fashena	ZFIN
Ken Frazer	ZFIN
Melissa Haendel	ZFIN
Doug Howe	ZFIN
Sridhar Ramachandran	ZFIN
Erik Segerdell	ZFIN
Ceri VanSlyke	ZFIN