FOOPS!: An Ontology Pitfall Scanner for the FAIR principles

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This document describes FOOPS, an ontology validation service that checks ontologies for adherence to the FAIR principles. FOOPS tests ontologies against criteria related to findability, accessibility, interoperability, and reusability. It provides explanations for test failures to help users improve their ontologies. FOOPS validation results include an overall FAIRness score and coverage of FAIR categories to assess ontology quality, though there is no single threshold for what makes an ontology fully FAIR. The document demonstrates FOOPS and lists the types of tests it supports under each FAIR category. It invites feedback to help further improve FOOPS.

Ingénierie

FOOPS! An Ontology Pitfall Scanner for
the FAIR principles
Daniel Garijo, Oscar Corcho, María Poveda-Villalón
Ontology Engineering Group,
Universidad Politécnica de Madrid, Spain
DBpedia Day - Semantics 21
daniel.garijo@upm.es
@dgarijov

FOOPS! An Ontology Pitfall Validator for the FAIR principles. DBpedia Day, 9th September, 2021
The rise of the FAIR Data principles
2
Other guidelines:
● Guidelines for Transparency and
Openness Promotion (TOP) [2]
● Reproducibility Enhancement
Principles (REP) [3]
● ...
Data (initially) [1]
Research Software
Methods
Semantic artefacts
[1] Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. The FAIR Guiding Principles for scientific data
management and stewardship. Sci Data 3, 160018 (2016). https://doi.org/10.1038/sdata.2016.18
[2] https://www.cos.io/initiatives/top-guidelines
[3] Stodden, V et al Enhancing reproducibility for computational methods
https://www.science.org/lookup/doi/10.1126/science.aah6168

FOOPS! An Ontology Pitfall Validator for the FAIR principles. DBpedia Day, 9th September, 2021
FAIR in not new: Background in the Semantic Web
3
▪ Linked Data principles [1] and 5-star ranking
▪ LD Principles adapted to ontologies [2] [3]
▪ Best practices for accessing vocabularies [4]
▪ Tutorials for publishing vocabularies [5]
▪ FAIR
How does all come together?
☆ Available
☆☆ Machine readable
☆☆☆ Open format
☆☆☆☆ Use standards
☆☆☆☆☆ Link to other resources
1. Use URIs
2. HTTP URIs
3. Resolve and provide useful info
4. Link to other URIs
[1] https://www.w3.org/DesignIssues/LinkedData.html
[2] https://bvatant.blogspot.com/2012/02/is-your-linked-data-vocabulary-5-star_9588.html
[3] Janowicz, K., Hitzler, P., Adams, B., Kolas, D., Vardeman, I., et al.: Five stars of linked data vocabulary use. Semantic Web 5(3), 173–176 (2014)
[4] Best Practice Recipes for Publishing RDF Vocabularies. https://www.w3.org/TR/swbp-vocab-pub/
[5] Garijo, Daniel (2013): How to (properly) publish a vocabulary or ontology in the web. figshare. Journal contribution. https://doi.org/10.6084/m9.figshare.881824.v1

FOOPS! An Ontology Pitfall Validator for the FAIR principles. DBpedia Day, 9th September, 2021
▪ Validation service inspired by OOPS! (OntOlogy Pitfall Scanner)
▪ Designed to guide users
o Tests have an explanation
o Tests indicate potential errors
▪ Practical
o Based on years of ontology engineering practices at UPM
▪ Aligned to FAIR
FOOPS!: A Pitfall Scanner for the FAIR principles
4
Live demo: https://w3id.org/foops/

FOOPS! An Ontology Pitfall Validator for the FAIR principles. DBpedia Day, 9th September, 2021
FOOPS! in a nutshell
5
Enter a ontology URI

FOOPS! An Ontology Pitfall Validator for the FAIR principles. DBpedia Day, 9th September, 2021
FOOPS!: Getting the full report
6
Ontology metadata summary
FAIRness coverage by category
FAIRness overall score. Note: this
may be a quality indicator, but
there is no deﬁned threshold for
FAIRness.
FAIR Category
Check
Check description
Check coverage
Check explanation

FOOPS! An Ontology Pitfall Validator for the FAIR principles. DBpedia Day, 9th September, 2021
Summary of supported tests
7
Findable
● Ontology URI is resolvable
● Ontology URI is persistent
● Version IRI exists (and resolves)
● Ontology id is ontology URI
● Minimum metadata is available (e.g.,
title, description, version info, etc.)
● Ontology preﬁx is in registry
● Ontology is in registry
Accessible
● Ontology is available in RDF/HTML
(content negotiation)
● Ontology is in a registry (repeated)
● Ontology is URI is deﬁned in
HTTP/HTTPS
Interoperable
● Ontology is at least available in RDF
● Ontology reuses known vocabularies
for declaring metadata (DC, Schema,
PROV, etc.)
● Ontology extends other vocabularies
Reusable
● HTML representation of the ontology
exists
● Extensive metadata is provided with
the ontology
● Labels and descriptions exist for all
terms
● License is provided and resolvable
● Metadata includes provenance
information

FOOPS! An Ontology Pitfall Validator for the FAIR principles. DBpedia Day, 9th September, 2021
Questions?
8
Help us improve FOOPS!
Errors? (please be gentle)
New tests?
Suggestions?
Drop us a message:
foops@delicias.dia.ﬁ.upm.es
Twitter: @OOPSoeg
https://w3id.org/foops/

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(Credit to Varun Ratnakar and Yolanda Gil). The automation of important aspects of scientific data analysis would significantly accelerate the pace of science and innovation. Although important aspects of data analysis can be automated, the hypothesize-test-evaluate discovery cycle is largely carried out by hand by researchers. This introduces a significant human bottleneck, which is inefficient and can lead to erroneous and incomplete explorations. We introduce a novel approach to automate the hypothesize-test-evaluate discovery cycle with an intelligent system that a scientist can task to test hypotheses of interest in a data repository. Our approach captures three types of data analytics knowledge: 1) common data analytic methods represented as semantic workflows; 2) meta-analysis methods that aggregate those results, represented as meta-workflows; and 3) data analysis strategies that specify for a type of hypothesis what data and methods to use, represented as lines of inquiry. Given a hypothesis specified by a scientist, appropriate lines of inquiry are triggered, which lead to retrieving relevant datasets, running relevant workflows on that data, and finally running meta-workflows on workflow results. The scientist is then presented with a level of confidence on the initial hypothesis (or a revised hypothesis) based on the data and methods applied. We have implemented this approach in the DISK system, and applied it to multi-omics data analysis.

Automated Hypothesis Testing with Large Scale Scientific Workflows

dgarijo

Credit to Yolanda Gil. OntoSoft is a distributed semantic registry for scientific software. This paper describes three major novel contributions of OntoSoft: 1) a software metadata registry designed for scientists, 2) a distributed approach to software registries that targets communities of interest, and 3) metadata crowdsourcing through access control. Software metadata is organized using the OntoSoft ontology along six dimensions that matter to scientists: identify software, understand and assess software, execute software, get support for the software, do research with the software, and update the software. OntoSoft is a distributed registry where each site is owned and maintained by a community of interest, with a distributed semantic query capability that allows users to search across all sites. The registry has metadata crowdsourcing capabilities, supported through access control so that software authors can allow others to expand on specific metadata properties.

OntoSoft: A Distributed Semantic Registry for Scientific Software

dgarijo

OEG tools for supporting Ontology Engineering

dgarijo

Credit to Yolanda Gil. In this talk I provide an overview of the current state of the art for software description in geosciences, along with our approach to facilitate this task in OntoSoft, a distributed semantic registry for scientific software. Three key aspects of OntoSoft are: a software metadata ontology designed for scientists, a distributed approach to software registries that targets communities of interest, and metadata crowdsourcing through access control. Software metadata is organized using the OntoSoft ontology, designed to support scientists to share, document, and reuse software, and organized along six dimensions: identify software, understand and assess software, execute software, get support for the software, do research with the software, and update the software.

Software Metadata: Describing "dark software" in GeoSciences

dgarijo

Overview of the different approaches for addressing reproducibilities (using semantics) in laboratory protocols, workflow description and publication and workflow infrastructure. Furthermore, Research Objects are introduced as a means to capture the context and annotations of scientific experiments, together with the privacy and IPR concerns that may arise. This presentation was presented in Dagstuhl Seminar 16041: http://www.dagstuhl.de/16041

Reproducibility Using Semantics: An Overview

dgarijo

Slides of the presentation for my PhD dissertation. I strongly recommend downloading the slides, as they have animations that are easier to see in power point. The abstract of the thesis is as follows: "Scientific workflows have been adopted in the last decade to represent the computational methods used in in silico scientific experiments and their associated research products. Scientific workflows have demonstrated to be useful for sharing and reproducing scientific experiments, allowing scientists to visualize, debug and save time when re-executing previous work. However, scientific workflows may be difficult to understand and reuse. The large amount of available workflows in repositories, together with their heterogeneity and lack of documentation and usage examples may become an obstacle for a scientist aiming to reuse the work from other scientists. Furthermore, given that it is often possible to implement a method using different algorithms or techniques, seemingly disparate workflows may be related at a higher level of abstraction, based on their common functionality. In this thesis we address the issue of reusability and abstraction by exploring how workflows relate to one another in a workflow repository, mining abstractions that may be helpful for workflow reuse. In order to do so, we propose a simple model for representing and relating workflows and their executions, we analyze the typical common abstractions that can be found in workflow repositories, we explore the current practices of users regarding workflow reuse and we describe a method for discovering useful abstractions for workflows based on existing graph mining techniques. Our results expose the common abstractions and practices of users in terms of workflow reuse, and show how our proposed abstractions have potential to become useful for users designing new workflows".

PhD Thesis: Mining abstractions in scientific workflows

dgarijo

Publicación de datos y métodos científicos en investigación

dgarijo

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FAIR Workﬂows: A step closer to the Scientiﬁc Paper of the Future

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SOMEF: a metadata extraction framework from software documentation

A Template-Based Approach for Annotating Long-Tailed Datasets

OBA: An Ontology-Based Framework for Creating REST APIs for Knowledge Graphs

Towards Knowledge Graphs of Reusable Research Software Metadata

Scientific Software Registry Collaboration Workshop: From Software Metadata r...

WDPlus: Leveraging Wikidata to Link and Extend Tabular Data

OKG-Soft: An Open Knowledge Graph With Mathine Readable Scientific Software M...

Towards Human-Guided Machine Learning - IUI 2019

A Controlled Crowdsourcing Approach for Practical Ontology Extensions and Met...

WIDOCO: A Wizard for Documenting Ontologies

Towards Automating Data Narratives

Automated Hypothesis Testing with Large Scale Scientific Workflows

OntoSoft: A Distributed Semantic Registry for Scientific Software

OEG tools for supporting Ontology Engineering

Software Metadata: Describing "dark software" in GeoSciences

Reproducibility Using Semantics: An Overview

PhD Thesis: Mining abstractions in scientific workflows

Publicación de datos y métodos científicos en investigación

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Sheet Pile Wall Design and Construction: A Practical Guide for Civil Engineers. By Dr. Costas Sachpazis. A Technical Report provides information on Geotechnical Exploration and testing procedures, analysis techniques, allowable criteria, design procedures, and construction consideration for the selection, design, and installation of sheet pile walls. "Sheet Pile Wall Design and Construction: A Practical Guide for Civil Engineers" by Dr. Costas Sachpazis provides an in-depth look into the engineering, design, and construction of sheet pile walls. The book details geotechnical exploration, testing procedures, and analysis techniques essential for determining soil properties and stability under various conditions, including seismic activity. It also covers the impact of groundwater on wall design and offers methods for controlling it during construction. Practical considerations for confined space work and the use of emerging technologies in sheet pile construction are discussed. The guide serves as a comprehensive resource for civil engineers aiming to enhance their expertise in creating durable and effective sheet pile wall solutions for complex engineering projects.

Sheet Pile Wall Design and Construction: A Practical Guide for Civil Engineer...

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African Journal of Biological Sciences is an International peer-reviewed, Open Access journal that publishes original research articles as well as review articles in all areas of Biological Sciences. It operates a fully open access publishing model which allows open global access to its published content. This model is supported through Article Processing Charges. For more information on Article Processing charges click here. Its scope embraces Animal Sciences, Biochemistry, Bioinformatics, Biotechnology, Botany, Cell Biology, Developmental Biology, Ecology, Environmental Sciences, Ethno Medicine, Food Science, Freshwater Biology, Genetics, Immunology, Marine Biology, Microbiology, Molecular Biology, Physiology, Plant Sciences, Structural Biology,Toxicology,Zoology etc. It is essential that authors prepare their manuscripts according to established specifications. Failure to follow them may result in papers being delayed or rejected. Therefore, contributors are strongly encouraged to read the author guidelines carefully before preparing a manuscript for submission. The manuscripts should be checked carefully for grammatical, punctuation errors. All papers are subjected to peer review. All articles published in this journal represent the opinion of the authors and not reflect the official policy of the Journal of African Journal of Biological Sciences

Call for Papers - African Journal of Biological Sciences, E-ISSN: 2663-2187, ...

Christo Ananth

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Introduction to Multiple Access Protocol.pptx

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Structural Analysis and Design of Foundations: A Comprehensive Handbook for S...

Dr.Costas Sachpazis

Introduction and different types of Ethernet.pptx

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KubeKraft presentation @CloudNativeHooghly

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AKTU Computer Networks notes --- Unit 3.pdf

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Welcome to the April edition of WIPAC Monthly, the magazine brought to you by Water Industry Process Automation & Control. In this month's edition, along with the latest news from the industry we have articles on: The use of artificial intelligence and self-service platforms to improve water sustainability A feature article on measuring wastewater spills An article on the National Underground Asset Register Have a good month, Oliver

Water Industry Process Automation & Control Monthly - April 2024

Water Industry Process Automation & Control

Roadmap to Membership of RICS - Pathways and Routes

M Maged Hegazy, LLM, MBA, CCP, P3O

The Educational Administration: Theory and Practice publishes prominent empirical and conceptual articles focused on timely and critical leadership and policy issues of educational organizations. The journal embraces traditional and emergent research paradigms, methods, and issues. The journal particularly promotes the publication of rigorous and relevant scholarly work that enhances linkages among and utility for educational policy, practice, and research arenas. The goal of the editorial team and the journal’s editorial board is to promote sound scholarship and a clear and continuing dialogue among scholars and practitioners from a broad spectrum of education. Educational Administration: Theory and Practice presents prominent empirical and conceptual articles focused on timely and critical leadership and policy issues facing educational organizations. As an editorial team, we embrace traditional and emergent theoretical frameworks, research methods, and topics. We particularly promote the publication of rigorous and relevant scholarly work with utility for educational policy, practice, and research. The journal’s primary focus is on studies of educational leadership, organizations, leadership development, and policy as they relate to elementary and secondary levels of education. Examinations of leadership and policy that fall outside K-12 are considered insofar as there are meaningful connections to the K-12 arena (e.g., college pipeline). International comparative investigations are welcome to the extent they have implications for a broad audience.s.

Call for Papers - Educational Administration: Theory and Practice, E-ISSN: 21...

Christo Ananth

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