CleanUpMeeting09Agenda/

Agenda for October 2009 Cleanup meeting
Agree a process for OBI 1.0 release, clean up issues below for discussion:

Meeting info: The Cleanup workshop will be held in the 13th floor library of Blockley Hall. 423 Guardian Drive, Philadelphia, PA, 19104 except for Sunday, the first day, where we will meet in the 14th floor conference room. These are in the Penn Center for Bioinformatics. Parking is available in a secured parking garage at 38th & Walnut ($20 per day) and an open lot just pass the University Avenue bridge ($7 per day I think).

See http://www.cbil.upenn.edu/meetings/2009-10-15_BlockleyParking.png

Hotel info: If you plan to attend the clean up meeting in Philadelphia and need a place to stay, you may find difficulty in booking a room especially on Sat. Oct. 17 (our meeting is scheduled from Sunday Oct. 18 to Wed, Oct. 21). Not sure what's going on - perhaps the Philadelphia Film Festival?

Anyway, when I checked yesterday there were still rooms available at hotels near the airport on Sat. Oct. 17. There is a Marriott ( http://www.marriott.com/hotels/travel/phlar-philadelphia-airport-marriott/ ) attached to the airport but others close by. (try Google maps with "hotels near philadelphia airport")

To get into town, there is a train, the R1 that runs from the airport into Philly with a stop at Penn. http://www.septa.com/service/rr_schedules.html However, I can also give people rides as well.

For the rest of the dates there are B & Bs such as http://www.gablesbb.com/reservations.html Here's a site with other B & Bs. http://www.bedandbreakfast.com/philadelphia-pennsylvania.html

If you are feeling lucky, the two hotels nearest Penn are the Sheraton (http://www.philadelphiasheraton.com/) and the Inn at Penn (http://www1.hilton.com/en_US/hi/hotel/PHLIDHH-The-Inn-at-Penn-A-Hilton-Hotel-Pennsylvania/index.do). but these were booked when we checked.

CS

Meeting Agenda
Sunday 18 October


 * Manuscript Discussion - all to have reviewed prior to meeting and a new version will be available


 * Examine Tracker Items, progress, prioritize - add more if needed


 * Process, we will operate a cut off on discussions, so if we can't make a decision we will move on. Need to agree what this will be.

P9 Items

 * 2845352 	 ISA-tools use case
 * 2843699 	person/Homo sapiens in OBI
 * 2843677 	IAO section of paper
 * 2843658 	use of plurals in the manuscript
 * 2832693 	Clinical study use case
 * 2100531 	mixtures of chemicals in Chebi

P8 Items (need prioritizing)

 * 2877331 	helper classes related to device
 * 2875994 	reagent roles
 * 2872993 	change import order of use case
 * 2855265 	instument clean up
 * 2836360 	Review all necessary and sufficient conditions for accuracy
 * 2828871 	_cloning placeholder
 * 2613561 	action specification
 * 2570459 	Device setting
 * 2078795 	vector role (cloning and disease)
 * 1889390 	Objective vs. Objective-neutral Planned Processes

Paper Related P8

 * 2832725 	Supplementary Table of terms used in manuscript
 * 2832701 	Update of figure 1 in manuscript
 * 2845347 	Authorship, Affiliations, Funding

Release Related P8

 * 2843660 	calculate the no of classes etc for release
 * 2878327       curation status of OBI terms

General clean up items
 Remove _classname - placeholder classes 

e.g. _realizable entity, _under discussion

note: _realizable entity and other top level buckets are only there to provide an anchor for defined classes. I would vote in favor of keeping those "development helper" classes in a separate file, along with OWL2 bits and all things we don't want in the released file. Other example of unwanted things is disjoint between obsolete classes and bfo:Entity, as this may create inconsistencies for users importing OBI and somehow defeats the purpose of obsoleting classes.

 Remove editor notes 

some difference of opinion here, BP/HP want to remove these, AR thinks they add value MC: happy to distribute editor notes if those were cleaned up. I don't think that this will happen realistically, nor that it should be a priority before release, so I would vote for removing them.

 Resolve all obsolete term useage

should be done by next release, will need checking again

 Resolve classified tree wierdness

probably needs a manual check of defined classes

 Remove duplicates

e.g mass spec

 Decide what to do with issues relating to requests to modify other ontologies e.g. RO

resolve/workaround/leave?

 Check leaf nodes with a single child, and check there potential additional children

 Clean up quality branch (aka conferred/historical qualities) 

Release related items
Use of obsolete terms

Extracted from the deprecation policy google doc - Implement scripts to find obsolete classes by either: deprecatedClass/deprecatedProperty, "obsolete" curation status, or being a subclass (direct or inferred) of ObsoleteClass or ObsoleteProperty. Update all such cases to remove axioms other than the single subclassOf, to update the curation status, and, optionally, to mark as owl:deprecated. tracker item

 Resolve editor attribution 

 Check inconsistencies

 Produce a saved inferred version 

 Mireot terms 

anything mireoted should probably be up to date in OBI 1.0 - do we have means to check this?

Minor issues to resolve now
 Enforce curation status 

Two issues


 * 3.1. curation status is not up to date and needs to be for release
 * 3.2 review terms where curation status is really not complete and prioritise if any need to be done for release, and add to tracker

 Spellcheck, check for consistent class naming style

 Resolve cases where there are no logical/text definitions 

 Resolve inconsistent logical/text definitions

Clean up editor attribution policy is one editor's name per annotation property, using PERSON: xxxxxx