Feb2006 GO Ed report
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GO Editorial Office Report - February 2006
SourceForge items Items opened 75 Closed by editorial office 53 (note: no SF item closed outside GO-Ed. this month; see end of report for details and for non-GO-Ed contributors to items we closed) Items in progress, assigned to editorial office 74 See monthly report in CVS for ontology statistics. Highlights - Our visiting student, Erika, has made lots of progress learning the ways of GO curation. She has established a good working relationship with the neurobiology interest group, and made a number of additions and changes in the process ontology for nervous system development and functioning. She is also learning GOA's annotation procedures (with Emily Dimmer), and has started annotating glutamate receptors. - The GO office (both GO Eds and GOA) spent a day helping Jacqui White, who has recently joined Sanger to work on their mouse knockout project (see http://www.sanger.ac.uk/Teams/Team109/). She's been charged with choosing genes for the project to knock out, and was/is interested in using GO to help with the target selection. At some point she may also become interested in PATO's doings, since they'll need to document the knockout phenotypes. Content topics in progress: Sensu terms - ongoing discussion in GOC (from GO Eds, mainly Jen) MetaCyc and GO consistency (includes metacyc2go mapping) (Amelia, with TAIR curators, esp. Peifen Zhang and Christophe Tissier) Neurogenesis (Erika, with Jen and the neurobiology interest group) Neurotransmitter uptake and secretion (Erika, with Jen and the neurobiology interest group) Plant development terms (Jen, with TAIR curators and Pankaj Jaiswal) Content topics resolved: Several nervous system-related development terms (Erika, with Jen and the neurobiology interest group) Several small things for SourceForge items OBO-Edit working group update: Highlight: The 'webinar' held Feb. 7-8 was a huge success (despite two out of three technologies falling over due to the number of participants). Transcripts are available in the group mailing list archives, and will probably also be put on the web somewhere. We may run similar tutorial sessions in the future, and ... Inspired by the webinar success, we have instigated regular 'meetings' via IRC (and John is looking into other technological possibilities). These can include shorter demos of new (or old but underappreciated) features, cross-platform testing, discussions, etc. Decided that version 1.000-beta16 will be eligible for release once the User Guide is complete. Progress on test suites, both automated (John D-R) and manual (curators; compiled by Jen and Amelia) Looking into making tutorial 'movies' like this one from RCSB: http://www.rcsb.org/pdb/ Conferences/meetings GO tutorial (annotation, microarray analysis) at MUGEN course, Milan (Jane) Preparation for GO talk and tutorial for computing workshop at European Fission Yeast Meeting (Hinxton, mid-March) (Jane, Midori) A little bit more progress planning GO Users meeting at MGED9 - room booked for Sept. 10th (Midori) Posters for St. Croix meeting (all) Publication Book chapter in progress: 'Parasites and GO' for bioinformatics text book for parasitologists (Jane, with Matt Berriman) Annotation outreach (Jen) Submission of annotations by PseudoCAP (with David Hill, Emily Dimmer) AmiGO working group Conference call (Amelia, Jane) Web page mockups (Amelia) Some updates to documentation (Amelia, Jen) Some updates to web pages (Amelia) A few queries on the mailing list (Midori, Jane) The GO Bibliography now has 773 entries. Appendix 1: input from others on SF items closed this month 1382483 - Katica Ilic 1416285 - David Hill, Doug Howe 1334217 - David Hill, Doug Howe 1431624 - Becky Foulger, David Hill 1420504 - David Hill 1429280 - David Hill 1429350 - Becky Foulger, Doug Howe 1242580 - TAIR curators 1416461 - David Hill, Doug Howe 1415524 - Doug Howe 1237567 - Pascale Gaudet, Michelle Gwinn 1228979 - Russ Collins, David Hill 1012287 - Russ Collins, David Hill, Pankaj Jaiswal 1247046 - TAIR curators Appendix 2: SF items that touch on other OBO ontologies 1416285 - CL 1428581 - CL 1416461 - CL