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12-14 November 2024, Costa Rica and Online

RDA 23rd Plenary Meeting (RDA P23) | Sustainable Science

Vocabulary Services IG �(aka VSSIG, Vocabulary and Semantic Services IG): �All About Terms and Ontologies (You Can Help!)

Collaborative Notes: https://docs.google.com/document/d/1MhGaGDISwufM_vMEAY9XJV2GFRqs54XA �Vocabulary and Semantic Services IG: https://www.rd-alliance.org/groups/vocabulary-services-interest-group

RDA P23 Collaborative Notes- IG (aka VSSIG, Vocabulary and Semantic Services IG): All About Terms and Ontologies (You Can Help!).docx

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Agenda

  • VSSIG Introduction for new participants – 10 minutes (Alexandra Kokkinaki-remote)
  • I-ADOPT: Latest achievements and Activities – 10 minutes (Gwen Moncoiffe in person)
  • Metadata Task Group – 10 minutes (Clement Jonquet-remote)
  • FAIR Mapping WG Activities
    • SSSOM - 7 minutes (Nico Matentzoglu remote)
    • FAIR mapping group updates - 3 minutes (Yann Le Franc in person)
  • Working Session: Identifying and Prioritizing Evaluation Methods for Choosing Terms and Ontologies – 50 minutes (All of Us)

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Housekeeping for all attendees

Please complete the table Attendee Check-in to indicate your attendance in the Collaborative Notes: here

Reminder: The session is being recorded

There will be time for questions after each talk, so please:

Participants in the room ask questions using the microphone

Virtual participants ask questions on the chat starting with @nameOfPresenter and following with your question

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VSSIG group: Who we are

by Alexandra Kokkinaki and the other VSSIG co-chairs:

Yann Le Franc, John Graybeal, Juliane Schneider

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Semantic artefacts and FAIR guiding principles

I2: (Meta)data use vocabularies that follow the FAIR principles

task forces, groups and projects focusing on

#semantic interoperability #semantics#ontologies #vocabularies #semantic artefacts

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The VSSIG past & present

  • Created in 2015

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  • 4 co-chairs: Yann Le Franc (2017), John Graybeal (2017), Alexandra Kokkinaki (2020), Juliane Schneider (2022)

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Vision

Our vision is to harmonize our ways of working/current practices with Semantic Web technologies through Knowledge and Expertise exchange across all domains.

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Join the group: https://www.rd-alliance.org/groups/vocabulary-services-interest-group/work-statement/

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Groups

Working group

  • I-ADOPT - B. Magagna/G. Moncoiffé/M.Stoica/A.Derajavu

Task Groups

  • Minimum Metadata Task Group - C. Jonquet
  • Terms and Concept Recommendations - J. Graybeal

BoFs

  • BoF – FAIR Mappings – Let’s start working

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Collaboration

Focus on collaboration

  • Other RDA Working Groups and Interest Groups
  • With you
  • With other projects

where semantics are involved

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I-ADOPT: Latest achievements and Activities�

Gwenaëlle Moncoiffé

12-14 November 2024, Costa Rica and Online

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Outcome:

Motivation:

  • Addressing the “I” of FAIR
  • Enabling interoperability between existing terminologies
  • Promoting the use of FAIR terminologies to annotate research data with well identified, unambiguous and machine-readable vocabularies

Led by a core group made of 4 co-chairs (Barbara Magagna, Gwenaëlle Moncoiffé, Anusuriya Devaraju and Maria Stoica) plus Sirko Schindler and Alison Pamment, with regular contributions from many others.

“InteroperAble Descriptions of Observable Property Terminologies”

The RDA I-ADOPT Working Group�Active work: 2019-2021 - Status: Maintaining Deliverables

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  1. Descriptions should be human and machine-readable
  2. Descriptions should be explicit and sufficient
  3. Use of semantic artefacts
  4. Use of I-ADOPT ontology
  5. Reuse of I-ADOPT aligned terminology

RDA I-ADOPT recommendations�DOI: 10.15497/RDA00071�

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The I-ADOPT Ontology �https://w3id.org/iadopt

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  1. The I-ADOPT Challenge
  2. Regular meetings to discuss implementations, priorities
  3. On-going work of I-ADOPT adoption at RI levels as part of European projects >> Opportunities to test interoperability (e.g. Envri-Hub-Next)
  4. Interactions with FAIR mappings WG
  5. Interest in I-ADOPT as an OGC standard
  6. Service development for annotation (e.g. PARC, FAIR2Adapt, NFDI4Earth, based on rag - retrieval augmented generation- LLM approaches and NLP techniques)
  7. Activities related to methods and protocols

Highlights of latest activities�

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When? Challenge 1 (16-29 Sept 2024), Challenge 2 (14-18 Oct 2024)

How many participated? 24 people/16 groups/different domains, but all data scientists

What was the purpose?�Reveal similarities and differences in the way different people use the I-ADOPT Framework to describe the same set of variables (30 variables in total)

What are the outcomes?

  • Opportunity to improve the framework and guidelines
  • Provide insights to develop a semi-automated I-ADOPT variable annotation service

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The I-ADOPT Variable Modeling Challenge�https://i-adopt.github.io/challenge.html�

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First Challenge:

provided variables: 30

counted variables: 10 best

winner principle: highest scores

challenge period: two weeks

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analysis: the more people model the better is their result

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Second Challenge:

provided variables: 10 (highest variance)

counted variables: 5 of high quality > 12pts

winner principle: all with 5 quality variables

challenge period: 5 days

Add. material: DO’s and DON’Ts

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analysis: Modelling tips help to make less errors, but the result is better the more is modelled

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First versus Second Challenge

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The I-ADOPT Variable Modeling Questionnaire�Answers from the participants�

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“some terminologies don’t resolve”

“providing meaningful labels”

“several options to model”

Why is I-ADOPT useful?

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  • FAIRify data
  • FAIRify metadata
  • Manage semantic artefacts
  • Manage data repositories
  • Harmonise digital objects
  • Make data reusable
  • Integrate data

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I-ADOPT Core team:

- Barbara Magagna (GO FAIR Foundation, NL)

- Gwenaëlle Moncoiffé (National Oceanography Centre - British Oceanographic Data Centre, UK)

- Anusuriya Devaraju (CSIRO, AU)

- Maria Stoica (University of Colorado, Boulder, US)

- Sirko Schindler (German Aerospace Center, DE)

- Alison Pamment (Centre for Environmental Data Analysis/Sience and Technology Facilities Council, UK)

External reviewers:

- Markus Stocker (TIB - Leibniz Information Centre for Science and Technology, GER)

- John Graybeal (Information Technology Consultant, US)

- Rob Atkinson (Open Geospatial Consortium, AU)

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The I-ADOPT Challenge: Reviewer Team�

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Challenge material:

- An introduction video to the I-ADOPT Framework

- A step-by-step guide for creating an I-ADOPT compliant variable description (video)

- Instructions for submitting modeled variables including participation and scoring rules (slides)

- The list of variables to be selected

- A questionnaire for background information about participants

Submission formats based on templates:

- human readable: Excel, text�- machine-readable: nanopublication, turtle

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The I-ADOPT Challenge: Material prepared

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Evaluation sheet includes:

  • list of variables, list of participants
  • scoring reference, criteria
  • all modelled variables as provided by Challenge participants and represented in Excel and evaluated accordion to the criteria
  • all modelled variables by core teams
  • agreed models and scoring results

I-ADOPT Challenge variables visualzed in the I-ADOPT Variable Examples repository

GitHub issues for discussing variable models

The I-ADOPT Challenge: Results

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First Challenge:

1st prize - €400 plus 2 virtual attendance fees for RDA 23: �Anne Fouilloux and Jean Iaquinta (212.75 points)

2nd prize - €300 plus 1 virtual attendance fee for RDA 23: �Andrea Tarallo, Martina Pulieri, Christina Di Muri, and Jessica Titocci (208.5 points)

3rd prize - €200: �Jörg Klausen, Morgan Silverman and Gao Chen (170.6 points)

The RDA TIGER Programme sponsored the attendance fees for the winners.

Qualified for the Second Challenge getting each €100:

Margherita Martorana, Samantha Blakeman, Petra ten Hoopen, Naouel Karam, �Juliana Menger, Saurav Kumar, and Norbert van Dijk

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The I-ADOPT Challenge: Winners!

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Metadata Task Group (Clement Jonquet)

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Metadata for Ontology Description and Publication Ontology

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Main focus of this task group was/is to develop MOD, as standard vocabulary to describe semantic artefacts.

⇒ https://github.com/FAIR-IMPACT/MOD

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Work done since 2022 in the context of the EOSC project FAIR-IMPACT

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MOD

  • Presented several time at RDA VSSIG (MOD 2)

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  • Extension / profile of DCAT2

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  • To describe any type of semantic artefacts (from metadata schemas to terminologies, thesauri, ontologies, etc.)

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MOD example

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Now MOD v3.2

  • Multiple design issues discussed and decided in MOD 3

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  • Now properties available to describe each objects including the mod:SemanticArtefactCatalog

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  • FAIR-IMPACT’s M4.3 - Specification of semantic artefact description

https://dx.doi.org/10.5281/zenodo.10725304

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MOD-API - specification of an API for semantic artefact catalogues

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  • FAIR-IMPACT’s D4.3 - Specification of shared metadata description of semantic artefacts and their catalogues including common reference API
  • https://dx.doi.org/10.5281/zenodo.12579779

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  • https://github.com/FAIR-IMPACT/MOD-API/
    • Describes the HTTP calls to implement so that multiple SACs can speak the same language
    • Relies on RDF, OWL, SKOS and MOD too to specify the objects to return
    • Objects being described with MOD listed metadata properties or more….

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A Simple Standard for Ontological Mappings 2024:

A quick guide for getting started with publishing better entity mappings @ RDA’s 23rd plenary

Contributors: Alasdair Gray, Alex Wagner, Amelia L. Hoyt, Andrew Williams, Anita Caron, Anne Thessen, Benjamin M. Gyori, Bill Baumgartner, Cassia Trojahn, Charlie Hoyt, Chris Mungall, Chris T. Evelo, Christopher Chute, Clement Jonquet, Damien Goutte-Gattat, Damion Dooley, Davera Gabriel, David Osumi-Sutherland, Emily Hartley, Ernesto Jimenez-Ruiz, Harold Solbrig, Harry Caufield, Harshad Hegde, Henriette Harmse, HyeongSik Kim, Ian Braun, Ian Harrow, James Malone, James McLaughlin, James Overton, James P. Balhoff, James Stevenson, Javier Millán Acosta, Jiao Dahzi, Joe Flack, John Graybeal, Jooho Lee, Julie McMurry, Kori Kuzma, Kristin Kostka, Lauren Chan, Melissa Haendel, Melissa Haendel, Monica Munoz-Torres, Nicolas Matentzoglu, Nicole Vasilevsky, Nomi Harris, Núria Queralt-Rosinach, Sabrina Toro, Sebastian Koehler, Shahim Essaid, Sierra Moxon, Simon Jupp, Sophie Aubin, Sue Bello, Sujay Patil, Sven Hertling, Thomas Liener, Tiffany Callahan, Tim Putman, Vinicius de Souza, William Duncan

https://w3id.org/sssom

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What are entity mappings?

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“Friedreich's Ataxia”

OMOP:441554

Entities are symbols, such as codes in a terminology, classes in an ontology, permissible values in a data model, identifiers in a database or simply strings in a text field that are intended to refer to a real world thing.

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The anatomy of a SSSOM-style semantic entity mapping

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are insufficient

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SUBJECT

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PREDICATE

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OBJECT

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�subject_id:

EFO:10000070

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�object_id:

MONDO:0006071�

�object_label:

adenofibroma�

�subject_label:

Adenofibroma�

�predicate_id:

skos:exactMatch

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JUSTIFICATION

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mapping_justification: semapv:LexicalMatching

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subject_match_field: rdfs:label�object_match_field: oio:hasExactSynonym

match_string: adenofibroma

mapping_date: 2022-12-13

reviewer_id: orcid:0000-0002-7356-1779

mapping_tool: wikidata:Q64360017

confidence: 0.8

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JUSTIFICATION

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mapping_justification: semapv:ManualMappingCuration

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author_id: orcid:0000-0002-7356-1779

confidence: 0.8

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SSSOM aims to

Provide a simple model to capture mapping evidence and provenance

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mapping_set_id: https://w3id.org/sssom/commons/mouse-human/mappings/mp_hp_mgi_all.sssom.tsv

mapping_set_title: All mappings of MP terms to HPO terms generated by MGI

mapping_set_description: "Consolidated list of all HPO to MP mappings done by MGI…."

creator_id:

- orcid:0000-0003-4606-0597

license: https://creativecommons.org/licenses/by/4.0/

object_source: obo:hp

subject_source: obo:mp

curie_map:

HP: http://purl.obolibrary.org/obo/HP_

MP: http://purl.obolibrary.org/obo/MP_

orcid: https://orcid.org/

obo: http://purl.obolibrary.org/obo/

Mapping Table

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What entity mappings are covered?

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MONDO:0006071

Type 1: lexical token - identifier

Type 2: identifier - identifier

Type 3: complex

EFO:1000070

MONDO:0006071

adenofibroma

Hypertensive heart disease without congestive heart failure

modifies

Not

Congestive heart failure

AND

Hypertensive heart disease

Experimental

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SSSOM is not for data structure mappings / schema crosswalks

New kid on the blog: LinkML-Map for �FAIR schema crosswalks!�https://linkml.io/linkml-map/

PERSON:001 ;

rdf:type my:Person ;

my:Name “Chris Mungall” .

PERSON:001 ;

rdf:type schema:Person ;

schema:givenName “...?...” ;

schema:familyName “...?...” .

But of course we can use SSSOM metadata to annotate crosswalks!

subject_id

predicate_id

object_id

my:Name

skos:narrowMatch

schema:givenName

my:Name

skos:narrowMatch

schema:familyName

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???

We will integrate this with RDA FAIR Mappings effort!

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The FAIR mappings community aims to�Promote the creation of interoperable FAIR mapping registries

  • Entity mappings are the glue of the Web of Research Data
  • Curating mappings is hard and expensive
  • We are building a global community of practice to
    • Share interoperable mappings
    • Develop shared curation and metadata practices (trainings, documentation, etc)

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m1.sssom.tsv

m2.sssom.tsv

m3.sssom.tsv

b.sssom.tsv

Registry

Shared QC, � automatic reconciliation

Wrong mapping!

Collaborative curation

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SSSOM 1.0: The data model is now stable

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With support from 79 community members contributing 1230 comments, 154 pull requests and 13 releases over the past 4 years, SSSOM 1.0 was finally released in August 2024.

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2 functional, independent and interoperable implementations:

  • sssom-java: https://incenp.org/dvlpt/sssom-java/
  • sssom-py: https://github.com/mapping-commons/sssom-py

Database (Oxford), Volume 2022, baac035, �https://doi.org/10.1093/database/baac035

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Acknowledgements and call to action

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Funding

Phenomics First (NIH / NHGRI #1RM1HG010860-01): Spec, sssom-py CLI��Monarch (NIH / OD #5R24OD011883): outreach, knowledge graph integration

Bosch Gift to LBNL: sssom-py IO, testing, converters, tutorials

DARPA: Young Faculty Award W911NF2010255�(PI: Benjamin M. Gyori)

�

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�Community contributions: https://w3id.org/sssom

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Learn about SSSOM!

  1. Do a basic training
  2. Study the documentation

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Spread the word

  1. All data initiatives will at some point produce mappings
  2. Bake mapping standardisation into your FAIR Data Publication plan!

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Set up a SSSOM Mapping Registry for your community

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  1. Use our template to create a mapping registry with quality control checking
  2. Collaborate with other groups on your mappings!

Publish your entity mappings in SSSOM format and share with RDA FAIR Mappings WG

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  1. Starting point: SSSOM 5-Star mapping practices
  2. Publish in public version control system
  3. Let us know at https://bit.ly/rda-fair-mappings-issues

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FAIR Mapping WG

Yann Le Franc, PhD

CEO e-Science Data Factory/ Head of EUDAT Secretariat

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Where did we start?

Two workshops about mappings and crosswalks during the RDA P21/International Data Week conference

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  • Generic session on mappings aiming at presenting the ongoing work of the FAIR IMPACT and FAIRCORE4EOSC projects

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  • A Bird Of a Feather session presenting 13 potential usages of mappings and discuss the relevance of creating an RDA Working Group.

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Where did we start?

Two workshops about mappings and crosswalks during the RDA P21/International Data Week conference

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  • Generic session on mappings aiming at presenting the ongoing work of the FAIR IMPACT and FAIRCORE4EOSC projects

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  • A Bird Of a Feather session presenting 13 potential usages of mappings and discuss the relevance of creating an RDA Working Group.

LOADS OF COMMUNITY FEEDBACKS

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Where are we now?

  • Co-created by FAIR IMPACT and FAIRCORE4EOSC

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  • Under TAB Review

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  • Initial activities

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    • Bird of a Feather session during RDA P22

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    • First working meeting in November

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    • Bird of a Feather session during RDA P23 (“WG Kick-off”)

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Which problems do we address ?

  • Mapping are hard to find and reuse

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  • Mapping are scattered across version control systems

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  • Mapping are expressed in formats not meant for automated processing

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  • Meaning of the term mapping is context sensitive leading to ambiguity

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What are our planned outputs?

  • Technical recommendations to make FAIR Mappings and FAIRness evaluation grid

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  • Practical mapping framework and guidelines

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  • Harmonized mapping use case collection

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  • Mapping classification/ontology

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  • Generic exchange model and the associated metadata

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  • FAIR Mapping Knowledge Base

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Working Session: Identifying and Prioritizing Evaluation Methods for Choosing Terms and Ontologies (John Graybeal & OntoChoice Team)

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About the OntoChoice Project: �Evaluations for Choosing Terms and Ontologies

Project Goals

  1. Collaboratively document evaluation criteria for choosing terms and ontologies
  2. Provide proof of concept demonstrations/examples/framework for these criteria

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Work to Date

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Introducing Evaluations Team and Facilitators

  • John Graybeal (facilitator Breakout 1)
  • Anna Maria Masci (facilitator Breakout 2)
  • Hande McGinty (facilitator Breakout 3)
  • Asiyah Lin (facilitator Breakout 4)
  • Juliane Schneider (Zoom facilitator for team)
  • Alexandra Kokkinaki (roving facilitator)
  • Eric G Stephan
  • Aryan Dalal
  • Christian Kindermann
  • Muhammad (Tuan) Amith

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Planned Activity: What’s Happening Here?

  • Today we all work together to improve this document
  • Each breakout group will focus on a particular section
  • Breakout discussions may organize, define, or discuss the work
  • Contribute concretely with edits, additions, changes, or comments
    • Or just take notes
    • Escribe en inglés o español, podemos convertir después
  • Come back together at end to hear how it went

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Overview of Working Document

🟢 0A. Introduction

🟢 0B. Categories of Evaluation Criteria (Relevance, Popularity/Reuse, Best Practices, Governance/Intl)

🔶⭕ 1. Category Descriptions and Detailed Criteria: Relevance Group (John)

🟢🔶 2. Category Descriptions and Detailed Criteria: Popularity and Reuse Group (Anna Maria)

⭕ 3. Category Descriptions and Detailed Criteria: Best Practices and Analytics Grp (Hande)

🔶🟢 4. Category Descriptions and Detailed Criteria: Governance & Internationalization (Asiyah)

🔶 5. Existing Evaluation Systems, Technologies, and Models

⭕ 6. Recommended Evaluation Facets (from the list in captures 1-4)

🔶 7. Use Cases to Discuss

⭕ 8. Evaluation Guidance

⭕ 9. Future Tasks

🔶 10. Resources and Bibliography

🟢 : first-draft complete. (Additions/improvements still welcome.) 🔰 : useful text and guidance but needs work. 🔶 : outline topics/example only. ⭕ : little useful content.

Our�Focus�Today

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The Categories of Evaluation Criteria

  • Relevance (a weed-out: these must be satisfied to use the ontology or term)
    • Does the ontology/term address the necessary topic(s) and have necessary approval?
  • Popularity and Reuse
    • How well-loved is the ontology/term? How often has it been used by others?
  • Best Practices and Analytics
    • Does the ontology/term content follow best practices defined for these assets?
    • Does the ontology/term’s measured qualities (size, depth, width, detail, …) meet needs?
  • Governance and Internationalization
    • Do the ontology/term maintenance processes follow best practices?
    • Is the ontology/term actively maintained?
    • Does the ontology/term provide appropriate internationalized content?

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Breakout Plan

  • We will have breakout rooms for 4-5 chapters (#1 through #4 at least)
  • The Relevance Group breakout will be in the main auditorium (‘here’)
    • This room will have simultaneous translation into Spanish
    • Other breakout rooms will be English speaking only
    • We encourage remote English speakers to go to other breakouts (#2 or higher)
  • Writing in spanish is welcome in this exercise/these documents. �(Escribiendo en español está bien en este ejercicio/estes documentos.)
  • We will integrate and address all the breakout content after the meeting.

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Today’s Goals

✅ Expose participants to the project and its progress

  • Make the document better
  • Find things missing from the document
  • Provide new perspectives
  • Create more opportunities to contribute to and improve this resource
  • Reward contributors (you) for your contributions: credit

Create content and feedback about this document!

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What You Will Do (in 25 minutes!)

  • Decide which facilitated topic you care about most
  • If remote, go to that Zoom breakout session
  • Everyone: go to the corresponding shared document (next page)
  • Work with your breakout group to make that section better
    • Working alone is OK too—tell the facilitator to avoid conflict!
    • If your group has no facilitator, choose one from the team (fast)
  • If you contribute to the document, enter your name/ORCID at top
  • When breakouts end, stay for summary and to fill out a tiny survey
  • You can keep working on the document after the session completes

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BREAKOUT SESSIONS AND LINKS      

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Starred (*) breakouts are facilitated. Two-star (**) breakouts may be facilitated.

These links go to the breakout copy of that chapter. And choose your Zoom breakout session with the same title. (See this slide at link bit.ly/ontochoice.)

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  1. Relevance Criteria Breakout: What We’ll Do
  • Open bit.ly/ontochoice1. Note that the links below are also there.
    • Add your name to the authors list if you are willing to be cited
    • Add your initials to any substance changes you make, for future discussion/credit.
  • Read the introduction section. Do you understand what we are addressing?
  • There are three categories of Relevance Criteria. Do they make sense?
    • If you have knowledge or insight to add, start adding it.
    • Let’s discuss the content for each as appropriate.
  • Overall comments also welcome.

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Return from Breakout: How was that for you?

  • Summaries from facilitators
  • Please fill out this Menti for us…
  • Thank you for your participation in this product-building exercise!

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THANK� YOU

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