TitleIndex

This is an index of all pages in this Wiki.

See also:

" | ( | 2 | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | a | b | l | m | n | t
Include system pages | Plain title index | XML title index

"

"/Discussion"

(

(Initiated by Emek Demir)

2

2005-06-25 ISMB Face-to-Face Meeting
2005-07-01 BioPAX-Boston Meeting
2005-07-13 Conference Call
2005-08-03 Conference Call
2005-08-03 Conference Call Minutes
2005-08-05 BioPAX-Boston Meeting
2005-09-07 Conference Call
2005-09-07 Conference Call Minutes
2005-10-05 Conference Call
2005-10-05 Conference Call Minutes
2005-11-08 Conference Call
2005-11-08 Conference Call Minutes
2005-12-07 Conference Call
2005-12-07 Conference Call Minutes
2006-01-11 Conference Call
2006-01-11 Conference Call Minutes
2006-02-08 Conference Call
2006-02-08 Conference Call Minutes
2006-03-01 Conference Call
2006-03-01 Conference Call Minutes
2006-04-03 to 07 Informal Workshop on formal semantics for BioPAX at Manchester
2006-04-12 Conference Call
2006-04-12 Conference Call Minutes
2006-05-03 Conference Call
2006-05-03 Conference Call Minutes
2006-06-07 Conference Call
2006-06-07 Conference Call Minutes
2006-07-05 Conference Call
2006-07-05 Conference Call Minutes[1 attachments]
2006-07-19 Conference Call
2006-07-19 Conference Call Minutes
2006-09-06 Conference Call
2006-09-06 Conference Call Minutes[1 attachments]
2006-09-27 Conference Call
2006-09-27 Conference Call Minutes[1 attachments]
2006-10-25 Conference Call
2006-10-25 Conference Call Minutes
2006-12-06 Conference Call
2006-12-06 Conference Call Minutes
2006BioPAXSmithBoston
2007-01-10 Conference Call
2007-01-10 Conference Call Minutes
2007-02-14 Conference Call
2007-02-14 Conference Call Minutes
2007-03-7 Conference Call
2007-05-2 Conference Call

A

About BlackBox Pathways
About Cardinality Restrictions In OWL
Activity Center Algorithm
Alan Ruttenberg
Alan Ruttenberg/Re-expressing a use case

a

alanr

A

Alanr Level 2 or 3 Proposal
Alanr Level 2 or 3 Proposal/association, new subclass of interaction
Alanr Level 2 or 3 Proposal/Binding representation
Alanr Level 2 or 3 Proposal/Binding site representation
Alanr Level 2 or 3 Proposal/Cellular location differences from my previous version
Alanr Level 2 or 3 Proposal/Classes would be better
Alanr Level 2 or 3 Proposal/Complex components are not complexes
Alanr Level 2 or 3 Proposal/Differences between previous examples
Alanr Level 2 or 3 Proposal/geneIdentifyingProteinXref
Alanr Level 2 or 3 Proposal/generics, maybe
Alanr Level 2 or 3 Proposal/How & why reorganize the top level
Alanr Level 2 or 3 Proposal/Initial email
Alanr Level 2 or 3 Proposal/intrinsicStateVariable and extrinsicStateVariable
Alanr Level 2 or 3 Proposal/Known bugs
Alanr Level 2 or 3 Proposal/modified true-false
Alanr Level 2 or 3 Proposal/Parallel hierarchies undesirable, confusing, removed
Alanr Level 2 or 3 Proposal/PSI-MI vocabulary migration summary
Alanr Level 2 or 3 Proposal/Representation of state
Alanr Level 2 or 3 Proposal/Representation of stoichiometry
Alanr Level 2 or 3 Proposal/Room for growth
Alanr Level 2 or 3 Proposal/State variable properties
Alanr Level 2 or 3 Proposal/Still missing: evidence types, cell types, tissue types
Alanr Level 2 or 3 Proposal/Undesirability of openControlledVocabularies
Alanr Level 2 or 3 Proposal/Unrepresentable currently: e.g. cleavage - what to do about it
Alanr Level 2 or 3 Proposal/Why and how to track a physical entity
AlanRuttenberg
Andrea Splendiani
AssociationPattern
AttachmentAssociation
Authority Of Pages
Authority Of Pages/Discussion
Authorship and Acknowledgement Guidelines

B

Background on Reasoners[1 attachments]

b

bader
bader/WorkSpace
best practices

B

Binding Sites
BioBase (transpath, transfac) priorities
Biological software supporting BioPAX
BioPAX Database Conversion Status[2 attachments]
BioPAX Development Process Goals
BioPAX Format Validation
BioPAX Governance
BioPAX Governance/Annotation
BioPAX Governance/Discussion
BioPAX inspired ontology[2 attachments]
BioPAX ISMB 2005 Meeting Agenda
BioPAX ISMB 2005 Meeting Participants
BioPAX Level 2 feedback[1 attachments]
BioPAX Level 2 feedback/BioPAX namespace issue
BioPAX Level 2 feedback/Naming Suggestions
BioPAX Level 2 Future Compatibility
BioPAX Packaging Recommendation
BioPAX People Pages
BioPAX Use & Deployment Issues
BioPAX validator
BioPAX web resources
BioPAX Workgroup Coordination
BioPAX-OBO
BioPAX-OBO-Memorandum
BioPAX-SBGN Mapping
BiopaxBostonMinutes
BioPAXLevel2MaintenanceRelease1
BioPAXMan Proposal
BioPAXWorkplanProposal-text
BOF meeting

C

CategoryDefinition
ChristianLemer
Class vs. instance representation example
Committees and Delegation Policy
Committees and Delegation Policy/Discussion
CommunityDevelopmentProcess
CommunityProcessDiscussion
CommunityProcessDiscussion/Discussion page
ConceptualGraph
ConferenceCall-17-03-2006
ConferenceCall-22-03-2006
ContentClarityCoverage
Converting OWL To UML[1 attachments]
CorePhysicalOntologyGuide
CSHF2Fmeeting[12 attachments]
CSHF2Fmeeting/Agenda1
CSHF2Fmeeting/Agenda2
CSHF2Fmeeting/Day1Notes
CSHF2Fmeeting/OrganizationMeetingNotes
CSHF2Fmeeting/See a photo[1 attachments]
CurrencyMetabolites
Current Ontology Development Issues
Current Ontology Development Issues/Discussion

D

DanCorwin
DatabaseRegistry
DatabaseRegistry/Discussion
DebuggingTheBugMetabolicExample200606[1 attachments]
Direct/Indirect Interaction
Discussion of Committees and Delegation Policy
DXTrackWorkplan

E

EditorGroup
Emek Demir
Example test cases
Explanation of OWL BioPAX rdf:RDF Header
External Controlled Vocabularies

F

FAQ
First State Subgroup Recommendation Draft (html)
Float versus Double (Initiated by Emek Demir)
FrankSchacherer
FrontPage
Funding Reporting
Funding Reporting/Discussion
Funding Reporting/Sep2005ProgressReport

G

Geeta Joshi-Topé
Gene Regulation Proposal[7 attachments]
Gene Regulation Proposal/Discussion
GenericParticipants
GenericsProposal-Generics and everything else are classes[7 attachments]
GenericsProposal-Generics and everything else are classes/ModifiedIrrelevant[5 attachments]
GenericsProposals
Genetic Interactions[11 attachments]
Genetic Interactions/BINDWorkedExample[3 attachments]
Genetic Interactions/BioGRIDWorkedExample
Genetic Interactions/Discussion
Genetic Interactions/Discussion/Version 1 discussions
Genetic Interactions/FlybaseWorkedExample
Genetic Interactions/OldNotes
Get Involved!
Guanming Wu

H

HarshaKarur
Host-Pathogen Interactions
How do I load OWL files in Protege[3 attachments]
How to convert an OBO ontology to OWL
How to discuss a wiki page
How to propose a wiki page for group approval
How to view worked examples

I

Imre Vastrik
IndirectControlProposal[1 attachments]
IndirectControlProposal/Discussion
Informal session on BioPAX/OWL modeling
InohMolecularRoleInSkos
IsBiologyOpenWorld

J

JapanF2Fmeeting
JapanF2Fmeeting/Exemption of Taxation[11 attachments]
JapanF2Fmeeting/hackathon[1 attachments]
JapanF2Fmeeting/symposium
JapanF2Fmeeting/technical workshop[3 attachments]
JapanF2Fmeeting/technical workshop/Activity ideas
JapanF2Fmeeting/technical workshop/Activity ideas/Adding support for gene regulation
JapanF2Fmeeting/technical workshop/Activity ideas/Adding support for Generics
JapanF2Fmeeting/technical workshop/Activity ideas/Adding support for Genetic interactions
JapanF2Fmeeting/technical workshop/Activity ideas/Adding support for States
JapanF2Fmeeting/technical workshop/Activity ideas/BioPAX overview
JapanF2Fmeeting/technical workshop/Activity ideas/BioPAX underview
JapanF2Fmeeting/technical workshop/Activity ideas/Cell Designer
JapanF2Fmeeting/technical workshop/Activity ideas/Collecting difficult examples
JapanF2Fmeeting/technical workshop/Activity ideas/Converters
JapanF2Fmeeting/technical workshop/Activity ideas/Delta P
JapanF2Fmeeting/technical workshop/Activity ideas/Description Logic
JapanF2Fmeeting/technical workshop/Activity ideas/Discussion about administration of the project
JapanF2Fmeeting/technical workshop/Activity ideas/Discussion of representation (classes, instances, the unknown)
JapanF2Fmeeting/technical workshop/Activity ideas/Hackathon Intro
JapanF2Fmeeting/technical workshop/Activity ideas/How vs What
JapanF2Fmeeting/technical workshop/Activity ideas/Intro to OWL-RDF and OWL tools
JapanF2Fmeeting/technical workshop/Activity ideas/Introduction to technologies (RDF, OWL), tools (Protege, Pellet, Libraries, etc) and ontology modeling
JapanF2Fmeeting/technical workshop/Activity ideas/Introduction to the other people and their work
JapanF2Fmeeting/technical workshop/Activity ideas/Little languages for Pathway curation
JapanF2Fmeeting/technical workshop/Activity ideas/mentioned
JapanF2Fmeeting/technical workshop/Activity ideas/Pathway comparison
JapanF2Fmeeting/technical workshop/Activity ideas/Queries
JapanF2Fmeeting/technical workshop/Activity ideas/Report on Kegg Conversion
JapanF2Fmeeting/technical workshop/Activity ideas/Requirements
JapanF2Fmeeting/technical workshop/Activity ideas/Roadmap review
JapanF2Fmeeting/technical workshop/Activity ideas/Role of Pathway Ontologies
JapanF2Fmeeting/technical workshop/Activity ideas/Simulation and Modeling
JapanF2Fmeeting/technical workshop/Activity ideas/Using OWL Lite GO in BioPAX
JapanF2Fmeeting/technical workshop/Activity ideas/Using OWL Lite version of useful OBO files in BioPAX
JapanF2Fmeeting/technical workshop/Activity ideas/What's meant
JapanF2Fmeeting/technical workshop/Activity ideas/What's missing
JapanF2Fmeeting/technical workshop/Activity ideas/What's wrong
JapanF2Fmeeting/technical workshop/Activity ideas/What's wrong representaton
JapanF2Fmeeting/technical workshop/Activity ideas/Workshop Day1 Intro
JapanF2Fmeeting/technical workshop/Activity ideas/Workshop Day2 Intro
JapanF2Fmeeting/technical workshop/Jpf2fPresentations[16 attachments]
JapanF2Fmeeting/technical workshop/Materials
JapanF2Fmeeting/technical workshop/Materials/AcceptanceLetter
JapanF2Fmeeting/technical workshop/Meeting notes
JapanF2Fmeeting/technical workshop/Meeting notes/October 11, 2005
JapanF2Fmeeting/technical workshop/Meeting notes/October 17, 2005
JapanF2Fmeeting/technical workshop/Meeting notes/October 25, 2005
JapanF2Fmeeting/technical workshop/Meeting notes/October 27, 2005
JapanF2Fmeeting/technical workshop/Meeting notes/September 30, 2005
JapanF2Fmeeting/technical workshop/organizing committee
JapanF2Fmeeting/technical workshop/Post Meeting Survey[3 attachments]
JapanF2Fmeeting/technical workshop/Priority opinions
JapanF2Fmeeting/technical workshop/Priority opinions/RuttenbergPriorities
JapanF2Fmeeting/technical workshop/Reflections
JapanF2Fmeeting/technical workshop/Reflections/Gary Bader
JapanF2Fmeeting/technical workshop/Schedule
JapanF2Fmeeting/technical workshop/Schedule/Alan's schedule proposal 1
JapanF2Fmeeting/technical workshop/Schedule/Discuss
JapanF2Fmeeting/technical workshop/Schedule/Discuss/Alan's summary of feedback
JapanF2Fmeeting/technical workshop/Schedule/Gary's schedule proposal 2
JapanF2Fmeeting/technical workshop/Survey Results[3 attachments]
Jeremy Zucker
JeremyZucker
Joanne Luciano
JoanneUnderEval
Jonathan Rees
JonathanRees
JonathanReesDetroitNotes
Judy Brewer

K

KeggConversionSummary
Ken
KenFukuda
Known BioPAX representation issues
Known OWL validation issues with vowlidator

L

Late 2005 Proposal for BioPAX Development[1 attachments]
Late 2005 Proposal for BioPAX Development/Discuss
Late 2005 Proposal for BioPAX Development/Discussion with Emek 2005-12-20
Late 2005 Proposal for BioPAX Development/Meeting notes 2005-12-15
Late 2005 Proposal for BioPAX Development/Response
Late 2005 Proposal for BioPAX Development/Working groups proposal
Late 2005 Proposal for BioPAX Development/Working groups proposal/wgp comments
Level 1 and 2 Fixes
Level 2 Known Issues
Level 2 Release Candidate Feedback[1 attachments]
Level 2 Release Candidate Feedback/adoption nonadoption/v1 - alanr
Level 2 Release Candidate Feedback/adoption nonadoption/v2 - bader
Level 2 Release Candidate Feedback/adoption nonadoption/v3 - alanr
Level 2 Release Candidate Feedback/adoption nonadoption/v4 - bader - Luciano - Zucker
Level 2 Release Candidate Feedback/Complex components confusion
Level 2 Release Candidate Feedback/v1.0 Announcement
Level 2 Release Notes
Level 2 Release Notes/v0.9
Level 2 Release Notes/v0.92
Level 2 Release Notes/v0.93
Level 2 Release Notes/v0.94
Level 2 Release Notes/v1.0
Level Two Requirements
ListOfEasyFixes
LocalBadContent
LocalSpellingWords

l

locatedInCell Class Tree

M

Mailing lists
Matthew Horridge
Matthias Samwald
MichaelCary
MichaelCaryDetroitNotes
MichelDumontier
MoinMoin/InstallationsAnleitung
MoinPagesEditorGroup

m

molecular species

M

MSKCC cancer pathway database priorities

N

Natalia Maltsev
NoEmptyStringExample
NoReuseOntologyExample

n

noteOnVersioning

N

NotesFor2005-07-13CallByGary

O

Old validation list
OlivierHubaut
OlivierHubaut/CSS[4 attachments]
On The Issue Of Directness
OntologyDesignPatterns
Open Issue : Pathway Step
Open Issue : Removing PhysicalEntityParticipant
Open Issue: What's in a name
Open world versus closed world
Open world versus closed world/BijanInstructionsToCloseTheWorld
Open world versus closed world/minCardinality
OverlappingPoolsOfMolecules
OWL File Formats
OWLAndSemanticWeb
OwlStates[2 attachments]
OWLValidators page

P

PageD'Accueil
Past meetings
Pathway Related Data Models[4 attachments]
Pathway visualizers
Peter Karp
PhysicalEntityClassificationAndNaming (Initiated by Nicolas Le Novere)
Planned Validation tasks
Planned Validation tasks/UnusedInteractionDiscussion
Presentations and Publications[1 attachments]
Proposed list of updates for the biopax website
ProtegeTips
PSB2006 SW-for-lifesciences Discussion Session
PSB2006 SW-for-lifesciences Discussion Session/InvitationLetter
PSI-MI Conversion
PSI-MI in OWL[1 attachments]

Q

Quick Link to Travel Information[2 attachments]
Quick Link to Travel Information/ShortVersion

R

RDF-IDs in BioPAX
Reifying a property
Release Checklist
ReleaseToolsProposal
Removing PhysicalEntityParticipant
Removing PhysicalEntityParticipant/Discussion
Renaming utilityClass
Renaming utilityClass/Discussion
Representational Styles
RepresentingBiology
Requirements motivated discussion excerpts from Biopax-Discuss
RethinkingMetabolicRepresentation20006
Roadmap discussion

S

Self-Annotating Identifers
Semantic reengineering (OWL)
Skype Transcript 6 12 2006
SkypeInstructions
SmithWorkshopInformation
SmithWorkshopOrganization
SmithWorkshopPrecipitate
Software Development Tools
SRI F2Fmeeting[12 attachments]
SRI F2Fmeeting/PeoplePics[9 attachments]
SRI F2Fmeeting/WhiteBoards[6 attachments]
Stan's Comment
State Proposal Discussion July 2005[5 attachments]
StatesAndGenericsProposal[2 attachments]
StatesAndGenericsProposal/Discussion
StatesProposalOLD[5 attachments]
StateSubgroup
SuperHackathonNotes
SystemPagesGroup

T

Tasks and Decisions

t

tentative validator

T

The Turing Test of Biological Representation
TheCellComponentOntology
Tips on Using this Wiki
To OWL or not to OWL
TopicMap
TopicPattern

U

UriCvNamespaceProposalJune2006
UriCvNamespaceProposalJune2006/Discussion
UriCvNamespaceProposalJune2006/Inoh[4 attachments]
Use Cases
UseCases for BioPAX-Manchester
Using Pellet
Using Pellet/Check abox consistency
Using Pellet/Load an ontology
Using SWRL with BioPAX

V

Validation notes 2005-07-06
Validation notes 2005-07-19
Validator BioPAX Access via SPARQL
Validator BioPAX Access via SPARQL/CardinalityPrototype
Validator BioPAX Access via SPARQL/OneOfSeveralValuesPrototype
Validator code examples

W

Website maintenance todo
WholePartPattern
Why We Document Requirements

last modified 2005-04-27 17:07:35