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Yanning Chen

995 days ago
zhongh3@rpi.edu eScience Meeting 20150302.1100 Mon
Patrick W
  • General Information
Patrick W
  • Next Meeting
zhongh3@rpi.edu Please join my meeting, Mar 2, 2015 at 11:00 AM EST.
Dates and Speakers
Date Weekday Time Speaker Topic
Feb 02 Monday 11am ET Linyun Fu Ontology Interest Group
Feb 16 Monday 11am ET Stephan Zednik Vocabulary Services
Mar 02 Monday 11am ET NA Catchups & Discussion
Mar 16 Monday 11am ET Linyun Fu Linked Vocabulary Schema
Mar 30 Monday 11am ET
Apr 13 Monday 11am ET
Apr 27 Monday 11am ET
May 11 Monday 11am ET
Possible Speakers and Topics for the first week:
Patrick W Call In
Stephan Z
  • Stephan Zednik (remote)
  • Peter
Patrick W
  • Patrick (remote)
  • Around the room (5-10 minutes max) 
  • Anything following up from last week (active items)
  • Talk
  • Discussion (15-20 min max)
  • Summary and What's Next (3-5 min max)
Action Items from Last Time
Stephan Z
  • Stephan - find old proposal for update to PML and share with Patrick as example for proposal to update ontology
  • Stephan - write down previous ontology publication practices
Patrick W
  • Patrick - proposal for TW ontology change
  • Patrick - proposal for TW Ontology Best Practices working group
Linyun F
  • Linyun - initiate a mail thread on the [ontology] list on specializing the LDA ontology   (please expand LDA)
  • a mixture of rationale and implementation
Stephan Z
  • Review previous meeting's action items
Patrick W
  • DOAP (Description of a Project) - Software as a project
Action Items
Deborah M
Linyun F
  • Linyun Fu: Prepare a talk about LVA ontology design in two weeks.
  • make sure not to ignore Epimorphics' credit.
Patrick W
  • Use rpi handle system to generate handles for all of our instances
  • Would love to see someone look into purl and give a presentation!
953 days ago
anirudh p anirudh
  • Topics of Interests
  • vocabulary vesioning: Marshall X Ma  for SKOS, there are "active" and "inactive" annotations to indicate whether elements are part of the current ontology
Stephan Z
  • Stephan: there are?
Hao Z
  • Ontology versioning
  • versioning in software engineering
Stephan Z
  • Semantic versioning convention (for software)
  • major.minor.patch
  • major changes generally break backwards compatibility and usually involve interface or contract changes
  • minor changes generally add new functionality but do not break backwards compatibility
  • patch changes are generally bug fixes that do not make interface changes (but fix incorrect behavior)
Hao Z
  • difference from software engineering.
  • branching, different urls
  • ==> documentating ontologies
  • ==> an ontology in development for a small exercise?
  • stephan presentation (SKOS; versioning)
  • ==> PROV'O
  • ==> technology issues for the data set
  • versioning meriting from semantic tools, in RDF?
  • how to use provenance to describe versioning
  • other...?
  • Notes
Linyun F
  • Software versioning (major versions, minor versions, bug fixes...) does it work well with RDF versioning? What is missing? 
  • Versioning along with documentation and annotation
  • Difference between software and ontology 
  • Scope: ontology has global scope
  • Polymorphism not allowed in ontology for good reasons
  • NO Encapsulation in ontology (no private elements)
  • Software is defined by interfaces, ontology change is almost always interface change -- reasoning clients will break.
  • Annotating implications of a change to an ontology is hard.
  • How to define minor and major changes for ontologies (since almost every change in an ontology is considered a major (interface) change for software)?
  • Decoupled governance of ontology changes
  • e.g., OBO foundry governance arrangement
  • Use case: VSTO?
  • Benchmark/criteria for ontology evolution governance practices?
  • whether break client tools, how hard it is to fix these breaks, ...
  • Branching in ontology versioning
  • How datasets underpinned by an ontology are influenced if the ontology changes.
Possible ontologies
  • DCO ontology needs to be reviewed so could have a discussion on versioning
  • Still have not switched to VSTO version 3
  • TW Ontology changing the tw:Concept and incorporating skos:Concept
  • skos, versioning of vocabularies
1009 days ago
Patrick W Meeting Password - grasshopper - oh yeah, I remember now
And why is there one in the first place? i dont know - being removed
Stephan Z
  • Stephan Zednik (remote)
Deborah M
  • Deborah McGuinness
Patrick W
  • Patrick (remote) - easily amused
  • Ontology group following-ups
Linyun F
  • TWC ontology discussion -- Patrick need feedback NOW!
  • Need a proposal for upgrading the TWC ontology first.
  • Having a group of people interested in writing down ontology best practices.
  • A group for ontology best practices inside TWC.
  • content negotiation
  • where to put our ontologies
Linyun F
  • policies, general ones and the ones for specific projects
Stephan Z
Patrick W
  • Each agency has their own terms, own meanings, etc... 
  • Makes mapping difficult
  • And most are not machine readable. Some are on a laptop, in someone's mind, etc... So need to formalize the vocabulary
  • Patrick West Q: SKOS Concept Scheme Mapping - and previous screen - descriptions/definitions?
Linyun F
  • Linyun Fu Q: Encode in an ontology the common patterns found across multiple vocabulary services?
Action Items
Stephan Z
  • Stephan - find old proposal for update to PML and share with Patrick as example for proposal to update ontology
  • Stephan - write down previous ontology publication practices
Patrick W
  • Patrick - proposal for TW ontology change
  • Patrick - proposal for TW Ontology Best Practices working group
Linyun F
  • Linyun - initiate a mail thread on the [ontology] list on specializing the LDA ontology
1023 days ago
Speaker Linyun
Topic Ontology interest group
Linyun F Marshall (remote)
Linyun F Anirudh
Patrick W Yu Chen (Momo)
xixi L Xixi Luo(remote)
Linyun F Peter Fox
  • Introduction to eScience meetings
  • in the beginning of each semester we send invitation to the escience email list and ask everybody to choose a time for the meeting for the semester.
  • for every escience meeting there will be a short talk. at the beginning of the semseter we are asking people to fill out their proposed topics to talk about.
  • the escience meeting is not made as a project meeting, but more as a discussion of general esicence and also particular intersets.
  • every new semester we will have a new organizer/chair for the meeting
  • Around the room (10-15 minutes max)
  • Hao: 1st yr phd student, starting on DCO project
  • lingyun: 5th yr phd student,,automatic capturing of provenance in research publications
  • Corey: 2nd year at TWC. research qualifier. a new project in material science. he said he will talk about that in the future
anirudh p
Marshall M
  • yu chen "slash" momo:  deep carbon observatory infrastructure, single sign on
  • xixi: postdoc working for deborah (DataOne project)
  • marshall ma: 3rd yr postdoc, use of semantic technologies in data management and publications; geoinformatics
Congrui L
  • stephan: software engineer. projects: NOCV; RDS; Dark Metadata
  • Patrick: work for Peter since 2002. Projects: DCO; RDESC; infrastructure for the lab
  • Prof. Peter Fox:
  • Apurva: 1st graduate student in IT, working for DCO
Linyun F Introduction
  • eScience meeting is a science meeting, not a project meeting
  • a short talk at each meeting (15-20 min talk, 5-10 min discussion)
Congrui L
  • discuss interesting research topics
Linyun F
  • place to talk about problems you are stuck on, interesting ideas...
Around the room
Hao: Deep Carbon Observatory (DCO)
Linyun: Provenance capturing for research publications
Corey: Material Science & Engineering Ontology
Anirudh: Dark metadata,NOCV
Yu Chen/momo: DCO, mobile sensor system
Xixi: DataONE --- build a data sharing network for earth scientist
Marshall: The use of semantic web technology for data publication and management, quantitative and qualitative modeling of geospatial data
Stephan Z Stephan: DCO-DS (dev-ops, s2s), NOCV (vocabulary services, possible RDA interest group), RDS (VIVO & CKAN for RPI datasets), Dark Metadata, BEDI
Linyun F Patrick: DCO-DS, RDESC, lab infrastructure management
Apurva: new ITWS student on DCO.
Patrick W Projects
  • DCO-DS (Deep Carbon Observatory - Data Science)
  • Dark Metadata
  • RDESC - Resource Discovery for Extreme Scale Collaboration
  • ToolMatch - Service to match tools with datasets
  • OPeNDAP Provenance - OPeNDAP - open source data access software
  • SemantEco
  • Jefferson Project
  • BEDI
  • NOCV - vocabulary services
  • RDS (RPI Data Services)
  • DataONE
zhongh3@rpi.edu Ontology Interest group within the eScience group
  • a lot of ontologies involved in these projects of us
  • an informal mailing list where people can put topics and questions.
  • useful across multiple projects
  • inspiring each other
  • later in the semester we can lead a ontology TWed talk & discussion
Linyun F
  • how do we publish ontologies in the lab? as the first problem to discuss on the list
  • can we take "ontology of ontologies" as the interest group name
  • what does ontology mean to each person?
  • ontology definition: a specification of a shared conceptualization
  • useful over beautiful
Congrui L
  • a Cmap to get some ideas on what to do and what should I take care of while using ontologies
Patrick W
  • Possible Discussions
  • Publishing an ontology in the Tetherless World Constellation
  • Is the term ontology synonymous with schema
  • Making assertions about ontologies defined by someone else.
  • foaf:Person subClassOf rdesc:Resource
  • Is Ontology Software?
Linyun F
  • Patrick's experience with VSTO 1.0
Patrick W
  • The ontology was overkill-ish
  • restrictions
  • min/max
  • disambiguation
Linyun F
  • developed in Protege, which automatically generates java classes from the ontology
  • ontology -> explicit, take knowledge hidden in the code, people's mind out and make it explicit in ontologies
Patrick W
  • Too much explicit details in a triple store? Unmanageable. Too slow. A lot of people turn off inferencing. Turn off restrictions and disambiguation.
Linyun F
  • implementability, expressibility, maintanability triangle for ontology design
  • difference: graph database vs relational database
Marshall M
  • open world vs closed world?
  • relational database could be a restricted graph database, more compact
Linyun F
  • relational database factors out common edges shared by instances in the knowledge graph, thus more restriction on data, more compact storage.
  • graph database has more expressivity
Patrick W
  • difference between graph database and directed graph database???

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