Hackpads are smart collaborative documents. .

Marshall X Ma

544 days ago
Deborah M Discussion Topics
  • best practices google doc <get pointer>
  • just navigating around our github content related to this
Han W
  • where are our ontologies?  and related sparql endpoints
  • where are our ontologies?  and related sparql endpoints
Marshall M 20160526 eScience Meeting 
Patrick W
  • General Information
  • This Meeting
  • Previous Meeting
  • Next Meeting
Call In
Marshall M 1.  Please join my meeting.
2.  Use your microphone and speakers (VoIP) - a headset is recommended.  Or, call in using your telephone.
Dial +1 (408) 650-3123
Access Code: 333-351-829
Audio PIN: Shown after joining the meeting 
Meeting ID: 333-351-829
Patrick W Attendance
Marshall M Marshall Ma
Han W Han Wang
Ian Gross
Jim M Jim McCusker
anirudh p Hao Zhong
Deborah M Zhen Liu 
Sabita Acharya  (will be remote after this week)
Liyu Pan <panl2@rpi.edu>
Rui Yan
  • Henrique O. Santos <hensantos@gmail.com>   
  • Paulo Pinheiro at RPI <pinhep@rpi.edu>
  • katie chastain (already on list)
Peter F
  • Ahmed (on travel, on list)
  • Sophie Kolankowski (getting married!)
Marshall M
  • Propose and discuss topics and questions for the coming eScience meetings
anirudh p Location - Place, Event, geographical etc
Ontology Change Template - May not apply for some ontology
Minimum subset of the template that needs to be filled. 
Patrick W Action Items
anirudh p
  • Ontology evolution talk based on Linyun's Work
  • Semantics of Quality and Bias Representations
  • Location representations in PROV 
  • Insider's Threat - Rui
Deborah M Please add me to the list  (the first 5 people below are all working with deborah this summer)
Patrick W
  • rashidshabbir@gmail.com
anirudh p
  • grossi2@rpi.edu
  • sachar4@uic.edu
Deborah M
  • Zhen Liu <zl1471@nyu.edu>
  • Liyu Pan <panl2@rpi.edu>
Patrick W Potential Topics
  • ontology best practices
  • Github Repositories
  • ontology versioning
  • ontology annotation
  • content negotiation and discoverability
Deborah M
  • registering (and advertising) our ontologies
Patrick W
  • easily creating semantic content (ontology editors as well as instance editors)
Peter F
  • Location representations (Marshall and Peter from Vespucci last June)
Marshall M
  • can also relate to work of the 'Spatial Data on the Web' OGC-W3C joint WG
Peter F
  • Location in PROV-O (Marshall and Peter)
Stephan Z
  • ?is this related to the location representations bullet above? Yes.
  • W3C PROV definition of Location: A location can be an identifiable geographic place (ISO 19112), but it can also be a non-geographic place such as a directory, row, or column. As such, there are numerous ways in which location can be expressed, such as by a coordinate, address, landmark, and so forth.
Deborah M
  • Ontology evolution and curation among Big / Broad communities
995 days ago
Should be a creative commons license version 3
Patrick W A list of what we shouldn't use for a license, like gpl 1 or 2
    <dct:creator rdf:resource="&twi;EricRozell"/>
    <dct:contributor rdf:resource="&twi;PatrickWest"/>
    <dct:contributor rdf:resource="&twi;person/MatthewFerritto"/>
    <dct:contributor rdf:resource="&twi;person/NancyHoebelheinrich"/>
    <dct:contributor rdf:resource="&twi;Christopher_Lynnes"/>
    <dct:publisher rdf:resource="&twi;ESIPFederation"/>
Linking back to change discussions
Use rdfs:seeAlso to link to page
  • Discussion
Linyun F Semantic Versioning
Marshall M
  • You cannot use the same uri for an object if its meaning has a major change
Deborah M
  • do we have a list of the licenses we do NOT want and also candidates for good ones?
Stephan Z
  • Use these
  • CCv3
  • MIT?
  • avoid these
Deborah M
  • GPLv2   (adding the sentence of why would be great too - i think you said that all derivative works needed to use the same license)
Linyun F Identifier
  • The purpose of an identifier: uniquely identify a thing.
  • Example: the use of DOI and DCO ID -- use URI as suggested dereferenceable identifier.
  • How can the people using the old ontology know to use the new version?
Patrick W
  • Using purl
Linyun F
Stephan Z
  • Does each class and property in the ontology get a handle? (Peter - micro-citation)
Linyun F
  • What if classes and properties used in multiple ontologies change? How the downstream is impacted?
  • If a class changes, do all its subclasses inherit the change made to that class?
  • ---------> March 30th Meeting a recap
994 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!
967 days ago
Linyun F Linyun (sick, stay at home) 
Hao Z Hao (rest well Linyun!)
Benno Lee
  • Topics of Interests
  • DOAP (Description of a Project) - representing software and software versions
Patrick W
  • Use case 1 - User requests aggregation of 3 datasets to be returned as a netcdf file from OPeNDAP Hyrax (data server)
  • request handled by multiple modules within OPeNDAP Hyrax
  • used in generation of provenance for the request - response object derived from the 3 datasets
  • Use case 2 - On the TW servers we have different versions of different pieces of software installed and we want to keep track of what's installed where
  • PURL (persistent uniform resource locator)
Hao Z
  • find the artical on it
  • are the purls being parsed by a server-side or an actual url?
  • is it content negotiable
  • Examples:
  • Ontology Evolution (Versioning)
Hao Z
  • SYSE
  • -> ontology best practices hackpad
Patrick W
  • Never remove a concept or property
  • If a concept or property is modified then it receives a new URI, it's a new concept/property basically
Hao Z
  • major/minor changes
  • provenance/relationships/hierachials
Linyun F
  • "deprecated" sign
  • vocabulary vesioning: Marshall X Ma  for SKOS, there are "active" and "inactive" annotations to indicate whether elements are part of the current ontology
Hao Z
  • the triangle? anybody can paste a picture?
  • software, database, provenance, schema, ... split tasks
Patrick W
  • Use Cases
  • change the description of a concept
  • add a new concept
  • remove a concept
  • simple typo in a description
Hao Z
  • ontology evolution literature, ISWC, ESWC, ASWC conference proceedings
Patrick W
  • RDA has an interest group related to this
  • Data Management for the lab (Discussion)
  • what is data management? Is it part of data science? What all goes into the management of data? Backups vs. Archives?
  • what is data?
  • dspace vs ckan vs ???
  • Dataset ontologies (dcat. A new one from w3c? Others?)
Marshall M
Patrick W
  • DCAT from w3c
  • VSTO has concepts around datasets
Action Items from Last Time
  • Patrick: NOT YET - Use rpi handle system to generate handles for all of our instances
  • Patrick: More of a suggestion - Would love to see someone look into purl and give a presentation!
  • Notes
981 days ago
Mar 16 Monday 11am ET Linyun Fu Linked Vocabulary API
  • Stephan (remote)
Linyun F
  • Linyun
anirudh p
  • Anirudh
Patrick W
  • Patrick
Marshall M
  • Marshall
  • Action Items from Last Time (10-15 minutes max) 
  • Linyun Fu: Prepare a talk about LVA ontology design in two weeks.
  • make sure not to ignore Epimorphics' credit.
  • Patrick: NOT YET - Use rpi handle system to generate handles for all of our instances
  • Patrick: More of a suggestion - Would love to see someone look into purl and give a presentation!
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???

Contact Support

Please check out our How-to Guide and FAQ first to see if your question is already answered! :)

If you have a feature request, please add it to this pad. Thanks!

Log in