Workshop Vancouver 2008 action items

Action Items Vancouver

 * Completed AI at end of this page
 * Deadline for minor edits, or addition of major edits to the tracker Mar 1
 * ? = no deadline yet
 * Need numbering, grouping by date, deadlines checking
 * All coordinator call issues to next coord call Feb 13

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Unassigned action items
NONE!!!!

Action items moved into tracker

 * AI:Edit:waiting was moved next to acclimatization and is no longer a child of PA Needs to be resolved when time representation is resolved (not done) DL:Time will be on agenda Summer workshop - consider Inviting Uli Sattler (add to tracker)

http://sourceforge.net/tracker/index.php?func=detail&aid=1962586&group_id=177891&atid=886178
 * AI:TIME - needs to be discussed and a proposal produced for representing temporal events, waiting etc in OBI DL:Summer workshopdiscussion to start on tracker (assign MC, merge with previous)


 * AI: Daniel Schober to update naming conventions page to allow suffix role being allowed in role special case and also for cases in data transformation branch which are sensible e.g. sine_transformation DL:7 Feb Tracker for DS created

http://sourceforge.net/tracker/index.php?func=detail&aid=1889536&group_id=177891&atid=886178
 * AI:Resolve the difference between Investigation and ProtocolApplication - BP suggests that PA never tests a hypothesis and that Investigations can have hypotheses DL:Mar 1 add to OWL file (add to tracker, assign BP) hypothesis in tracker

http://sourceforge.net/tracker/index.php?func=detail&aid=1962584&group_id=177891&atid=886178
 * AI:Develop a use case that shows cross database integration using OBI and add a milestone for the long term plan. JW DL:Jul 1


 * AI: AR/BP/BS - will refine the analyte proposal. There are placement issues to resolve. DL:Mar 1 release (tracker 1866457)


 * AI:Relation Branch will develop a way to make it clear for relations using an annotation property (or similar) to make it clear which relations can be used at class and which can be used at instance level. This constraint is needed. DL:Mar 1 (entered into RO tracker 1949892 )


 * AI:move hypothesis, dt role, stat factor from role, add under new class specification suggest a new role - specifies? Plan/PA branch DL:Info Ontology?  TRACKER TO JF


 * AI:processes can't bear roles, objective is used instead for e.g. negative control - add to tracker. JF/JG DL:Feb 7  TRACKER TO JF


 * AI:Communities to send terms to instrument branch to improve coverage. BB will send an OWL file for BIRN microscopy and imaging. CK will review the file and reformat. TRACKER TO BB


 * AI:Edit:suggested edit new class role assignment with group assignment underneath it if PA can be distinct from a Planned Process PRS DL:Mar 1 TRACKER TO PRS


 * AI:Edit:Definition of PA defined as being carried out to modify or generate data or materials in an investigation. Issues still BP. DL:Mar 1 TRACKER TO BP


 * AI:biomaterial will attempt define in vivo, ex vivo etc as a defined class and see if this works, these may be at assay level not material level, and these will likely be processes PRS DL:Mar 1  TRACKER TO PRS


 * AI:MC/BB/JF will write up the explanation on Role, Function and what we understand about these for distribution and we will then develop a consensus on going forward on this. DL:Mar 1 (not OWL file) docs In Progress - Bill working in function - we will write a doc  TRACKER TO MC


 * AI:We will need to deal with Parameters instances such as voltage, use cases from Instrument, will be in qualities. MC will group terms on a google doc and work with PATO DL:Mar 1 term submission to MC's google doc - submitted to PATO beginning of march, but no feedback yet.  TRACKER TO MC


 * AI:Produce an example a Protocol acquired into ProtocolApplication from ArrayExpress - HP DL:Mar 1


 * AI:BS/AR will devolve organization ontology, document ontology and information entity to a new ontology in the future, these are too high level for OBI ASSIGNED TO BP


 * AI:BB will send the link to his modified BirnLex SW ontology to the data transformation branch ASSIGNED TO BB


 * AI: John Westbrook will provide us with top-level hierarchy (low number of terms) for incorporation into OBI. ASSIGNED TO ALAN TO EMAIL JW


 * AI: Cartik will share his annotations with OBI 'MC TO EMAIL


 * AI: AR will develop measurement proposal and circulate to OBI and Chris Mungall, Barry Smith, Michael Ashburner as this conflicts with "towards" relation in PATO, and derive a consensus. ASSIGNED TO ALAN Tracker to Alan to develop and circulate ' measurement proposal' . Discuss integration of information in general at workshop


 * AI:types can bear quality like things features and mathematical function and this is a workaround here where classes are created in OBI for math entities. Outside BFO so needs to be OBI and would mean that we don't need a relation. New class called feature - has_feature relates a type to a feature, all base, degree and number are features of type. DT branch and CC, AR, BS. 'Reassigned to JM

Completed Action Items
AI:Bi-weekly releases of the OBI merged file will be made in SVN, it will be versioned less than 1.0). This will require unit tests from Bill (another AI from this workshop), will be in OWL-DL, likely this will mean use of pellet. Will be released on 1 and 15 of each Month. First release will be on March 1. For release it must classify in pellet at a minimum. This will be a per 1.0 release. JG will provide his an xls version as well BB, MC, CK, JG DL:Mar 1, first release 2 first releases done - is OWL-DL and passes Pellet test

AI:Resolution of how to focus coordinators and also have useful community representation, and  also to consider advisor input CS  DL: 13 Feb, next coord call -DONE set up core coordinating committee

AI:When call minutes done, sent to list for branch or dev, coord, and name minutes from that date and that branch - All branch editor and or person hosting dev or coord call DL:immediate effect

AI:Dealing with multi branch issues - if these exist they will go into tracker and hence a dev call DL:Immediate

AI:MC will add stimulus to the tracker DL:Mar 1 (decision is to be added if need expressed)

AI:AR,BS will go to the relations ontology meeting in Denver to present our needs DL:May 19 (retire)

AI:AR will post the OBO release policy document and people will offer comment on if this is a good policy for OBI
 * DL:DONE. Deadline for comments Feb 15

AI:Edit:InformationEntity will be renamed plan, synonym RealizableInformationEntity
 * DL:DONE

AI:Edit:DigitalEntity->child of NonRealizableInfoEntity, Plan will be a sibling of NonRealizeableInfoEntity, both children of InfoEntity
 * DL: DONE

AI:EDIT:Objective now child of InfoEntity
 * DL:DONE

AI:EDIT:Define Objective add a definition, synonym is GOAL
 * DL:DONE

AI:Edit:re-defined material transformation - added to OWL file. .. is a protocol application where the objective is to produce output material from input material'
 * DL:DONE

AI:Edit:Check the definition of DataTransformation, MaterialTransformation, and all children of PA (except waiting moved) reworded for consistency. PA also redefined in terms of bring about objective of a protocol
 * DL:DONE

AI:BS/AR to explain why roles cannot be born by processes. DONE. We will use objective of planned process to state e.g. variables and then processes such as sham surgery are do not need to be bearers of roles., the objective of a sham surgery control is the objective. The process is independent of this
 * DL:DONE

AI:JW to look at use case docs and suggest some for stuctural biology
 * DL:DONE


 * AI:population now has material as a parent and not object aggregate as material is now a union of BFO things
 * DL:DONE

AI:Add imports and all related issues as an agenda item for the next workshop SS
 * DL:DONE

AI:Call the notes into the WIKI and make sure that they are all findable JM
 * DL:DONE, all in table now.

BB/MC will report of the resolution of the curation complete issues discussed elsewhere
 * DL:DONE

AI:Hospital should be added when Organization is added to OBI tracker MC
 * DL:DONE


 * AI: AR/BB/JF - BB will produce a TRUE role subset of the INOH Molecular Role ontology, which AR will review, and pass on to JF.

JM has reviewed DENRIE branch, CS has reviewed DT branch
 * AI: Branch/Individual review of other branches by March


 * AI: Develop a documentation plan for OBI and assign tasks JM/MC/BB.


 * AI:OBI coordinators should nominate 1 person to be OBO foundry associate editors - agenda item for a coordinators call CS 'DL:Mar 12 coord call. DONE - was discussed, candidates identified, question of more than 1 - waiting for more info to be resolved at a later call'


 * AI;Disjointness, currently incomplete. Strip all out and script adding back in. Al will be pairwise DJ apart from a couple of places in BFO where it's fuzzy AR/MC


 * AI:BS will resolve BFO issues reported to him.


 * AI:Works with Chebi to resolve roles for chemicals, submit to Chebi. JF/SS/PRS


 * AI:Approved relation branch terms will be sent to RO2 LF DONE


 * AI:branches to prioritize which relations are needed and tell role branch DONE


 * AI:Policy needs developing and take to a coord conference call DL:12 Mar Coord call (assummed to refer to authorship policy)


 * AI:PRS will put together something for discussion on Plan, PA and Protocol - will be discussed later this week (Plan and PA branch work will be merged into a single effort) DL:Mar 1


 * AI:AR/BS w DENRI. Is a 'variable' is a relation to a class or an entity DL:DONE


 * AI:issue that we need a quality like thing of 'Gifness' and how works with DENRI. could also be solved by using feature om OBI as above, again a work around BS/AR: DL:?When info ontology is tackled?  Current decision is to leave GIF as data format specification instance, but move the instances to a separate file.  Done: new file DataFormatSpecification.owl  People need to update their .owl and .repository files to include it 


 * AI:discuss within Instrument branch ,consequences for making artefact object a defined class only to avoid problems where there are biomaterials that are also human generated. DL:Feb 15  OR can we could keep artefact object and add classes underneath it use this strategy only for biomaterials, as we think all instruments will be artefact objects. Would be weird to have instrument next to protein. MC will communicate to instrument branch. Biomaterial branch are going with the defined class and will use reasoner to place terms in h'archy e.g. under artifact object and some other parent DONE


 * AI: proposal how to define material: material is union of BFO object, BFP object aggregate, BFO fiat object part. Is now the root for biomaterial and artifact which are defined classes and will help OBI be multi granular DL:Mar 1 OWL file DONE


 * AI:DT can do the gating examples as a defined class into the ontology - branch action item RS/RB/JM/PRS DL:Mar 1 DONE


 * AI:MC/JM/AR/DS to write up an OBI import/mapping strategy doc as described at the workshop as doc DL:Apr 1 Done: http://docs.google.com/Doc?id=dzprnmw_5fwg97rds 


 * AI:AR/JM/MC will work through a use case with the cell type ontology import needed for biomaterial and test this strategy and report on the results. This will be an OBI application ontology as soon as we start bringing into OBI DL:Apr 1  DONE


 * AI:develop a strategy for dealing with the OBO foundry ontologies and OBI application ontology if import works. Decision if we have that everything is done. DL:Workshop  DONE


 * AI:Two proposals for release notes, OWL file annotation property and SVN checkin logs, resolved as editor notes long, SVN short. DL:DONE


 * AI:custom google custom search box for OBI wiki will be requested from CS group CS DL:In progress, Apr 1 - DONE


 * AI:Wiki DENRI, Relations, Quality, Role need links to their term list files and or notes on the Branch Conf Calls DONE


 * AI:General feeling that there is no design whereby computing over h'archy depth is designed into OBI and it's not a good way to work with OBI at present MC will speak to EM about this DL:Mar 1 DONE


 * AI:An underscore will be added to each branches helper classes, each branch will deal with this themselves DL:Mar 1 OWL file  DONE


 * AI:Bioportal should point at the most recent version OBI-OWL merged file release so that progress is visible. We could release every 2 weeks, point at what changes in change log. Could be pull or push. Chris Stoeckert and Daniel Rubin. DL:15 Feb for mechanism, upload after Mar 1  DONE


 * AI:BP and AR will try and develop ProtocolApplication from Plan to evaluate whether this can be done automatically. This is a script to merge. Evaluation needs to be soon DL: Mar 1


 * AI:Protocol and ProtocolApplication branches will be merged. The OWL files for Plan, Protocol have been merged by AR. He will send instructions to the dev list DL: DONE files merged committed, PA list will be used, Alan will fix plan email to PA


 * AI:How do we embed OBI in different systems - AR wants as focus of a session this week DL: DONE


 * AI: JW will provide a link for PDBs attempt to deal with instrument and parts thereof to do this for beamlines JW DL: DONE


 * AI:Make the connection between the visulation between table and graph that comes out of this process currently that is in the DENRI branch. A cross branch issue. DT, DENRI. JM. DL:Feb 15  DONE


 * AI: CS The https://wiki.cbil.upenn.edu/obiwiki/index.php/QuickTerms-CrossProducts  proposal  as topic on agenda for next  developer call DL: February 15 - DONE - put on Feb 6 agenda.


 * AI: Develop a test plan for the OBI release, document and execute BB DL:Mar 15 (second release) In Progress (tracker http://sourceforge.net/tracker/index.php?func=detail&aid=1911447&group_id=177891&atid=886178)


 * AI:Definition of InformationEntity to be done by BS/AR/BB (tracker http://sourceforge.net/tracker/index.php?func=detail&aid=1950131&group_id=177891&atid=886178)

http://sourceforge.net/tracker/index.php?func=detail&aid=1950134&group_id=177891&atid=886178 http://sourceforge.net/tracker/index.php?func=detail&aid=1950135&group_id=177891&atid=886178 http://sourceforge.net/tracker/index.php?func=detail&aid=1950136&group_id=177891&atid=886178 http://sourceforge.net/tracker/index.php?func=detail&aid=1950137&group_id=177891&atid=886178 http://sourceforge.net/tracker/index.php?func=detail&aid=1950139&group_id=177891&atid=886178 http://sourceforge.net/tracker/index.php?func=detail&aid=1950140&group_id=177891&atid=886178 http://sourceforge.net/tracker/index.php?func=detail&aid=1950196&group_id=177891&atid=886178
 * AI:Take use cases and see if OBI can be used to complete these use cases, need some kind of template for this: DL:May 1 (add to tracker in including each use case)
 * RB:Flow cytometry use case
 * JM/HP:ArrayExpress use case
 * PRS/BII use case
 * BB:BIRN use case
 * JF SIFT use case
 * GenePattern use case (CS/HP) - HP contacted GenePattern who expressed interest
 * JG:Immunity use case

http://sourceforge.net/tracker/index.php?func=detail&aid=1950143&group_id=177891&atid=886178
 * AI: Developing a long term (5 year) management plan for the OBI grant - AR/BP/BS DL:Apr 1 (add to tracker, assign BP)

http://sourceforge.net/tracker/index.php?func=detail&aid=1950007&group_id=177891&atid=886178
 * AI:EDIT:evaluant is added as a role, RS will make a definition. It's the thing being evaluated DEF:An evaluant_role is the role played by a portion of material (including specimens and human subjects) that serves as the subject of study in an assay such that the output data describes a feature (quality..... e.g. "contains 10 pg/ml IL2") of the evaluant. DL:Def done, OWL file Mar 1 def tbd with RS


 * AI:use roles for e.g. buffer in (bio)material rather than hierarchy - BioMaterial Branch DONE


 * AI:Ontology annotation and release notes policy DONE


 * AI:AR will look into what are committing to in becoming a W3C group DONE


 * Coordinators/core dev will review March 1 release and any issues will be added to track for resolution and may be accepted via some process defined by the coordinators if there is conflict. DL:Mar 15   DONE - set up core coord committee


 * AI:Deprecation policy will be discussed on next coordinators call to allow others to comments. AR Proposal for discussion is that we use OBO foundry process, add an obsolete class. Issues with logical definitions and previous use of editor note for this CS  DONE


 * AI:RS will provide a clinical trial example of protocol DONE


 * AI:Alan will generate a list of problems and solutions with DENRI for discussion on a conference call. Info ontology. DONE Dealt with in calls


 * AI:BS will provide a better name for MeasurementUnit as Units pre-exist in the world outside data and so the name is bad. Result: Email send to Barry who is fine with MeasurementUnit for now; may revisit this later in the context of the overall measurement proposal. DONE


 * AI: DT branch will test objective, not role for e.g. normalization - might make things easier and practical consequences will not be huge: DT branch, Protocol DL:Mar 1 OWL file  'DONE - now handed over to plan and planned process

ActionItemsByDateDiscussed [category:Meetings]]