1. Towards Reusable
Research Software
Daniel Garijo Verdejo
@dgarijov
daniel.garijo@upm.es
Ontology Engineering Group
Departamento de Inteligencia Artificial
Facultad de Informática
Universidad Politécnica de Madrid

2. Reproducibility: Open Research Data, Software and Methods
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Scientific publication
Research Data Research Software Research Methods
EOSC Symposium: Infrastructure for quality research software

3. Challenges for (Re)using and Sharing Research Software
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• What does the software component do?
Which of its methods should I use?
• How to transform my data to use the
software component?
• How to interpret the results produced by
the software component?
• How to invoke the software component?
• How to configure the software component
with the right parameters?
• How to compare against similar methods?
Software designer
Software user
• How to ease capturing the
dependencies and installation
instructions of my software?
• How to encapsulate my software so
it can be used with other data?
• How to describe my software so it
can be used by others?
• How to test if my software is ready
to be used by others?
EOSC Symposium: Infrastructure for quality research software

4. Community Initiatives and Standards
• Describing Research Software
• Schema.org & Codemeta
• Common Worflow Language (I/O)
• Packaging Research Artefacts (incl. software)
• Research Objects (RO-Crate)
• Aggregators (OpenAIRE, EOSC)
• General (e.g., Zenodo) &
domain-specific registries
• Scicodes (https://scicodes.net/)
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Nine Best Practices for Research Software Registries and Repositories: A Concise Guide https://arxiv.org/abs/2012.13117
EOSC Symposium: Infrastructure for quality research software

5. Adopting annotation vocabularies: where are we at?
Software metadata is not abundant machine readable
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EOSC Symposium: Infrastructure for quality research software
Can you please describe your
software component with metadata?
I already did! Did you read the
project readme?
Did you see the online
documentation?
Perhaps the you saw the
paper?
Many domain-specific registries are curated by
hand by experts

6. Automated Software Metadata Extraction
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SOMEF
SOftware Metadata
Extraction Framework
https://github.com/KnowledgeCaptureAndDiscovery/somef/
[Mao et al 2019]: SoMEF: A Framework for Capturing Software Metadata from its Documentation. 2019 IEEE BigData REU Symposium. Los
Angeles, 2019
EOSC Symposium: Infrastructure for quality research software
Code repository
(readme)
Machine-readable file with software metadata:
• > 20 common metadata fields
• Installation instructions, description, invocation
command, license, author, citation, requirements,
examples, documentation, notebooks, etc.
• Analysis of readme and supp. Files (e.g., notebooks,
Dockerfiles)
• JSON, RDF(graph), Codemeta, RO (in progress)

7. Leveraging Software Metadata to create Knowledge Graphs
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Explore input/output variables (interoperability)
Explore Software I/O files
(composition)
Knowledge Graphs with can link RS and its
components.
OKG-Soft: machine-readable Software Metadata:
• (From Schema.org) Attribution, license, funding,
usage examples...
• Executable software components
• Software invocation
• Input & output files, variables and units
• Containers used to encapsulate and run software
components
• Parameter validation and suggestion
[Garijo et al 2019]: OKG-Soft: An Open Knowledge Graph with Machine Readable Scientific Software Metadata. International
Conference on eScience, San Diego, USA. 2019
EOSC Symposium: Infrastructure for quality research software

8. Conclusions
Research Software Metadata should be actionable and useful for:
• Understanding the differences between two or more software
components
• Help portability (ROs)
• Add components in workflows (CWL + ROs)
• Help linking similar software methods
• Build automated comparison benchmarks
• Reduce the time needed to understand and adopt an existing
software component
• Author credit
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EOSC Symposium: Infrastructure for quality research software

9. Questions?
Let's create machine-actionable software metadata
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Image credit: https://icons8.com/icons/
+
findable
portable
comparable
executable
reusable
Code +
documentation
Automated
extraction
Knowledge
Graphs
EOSC Symposium: Infrastructure for quality research software
Acknowledgements: Yolanda Gil, Deborah Khider, Varun Ratnakar, Maximiliano Osorio,
Hernan Vargas, Oscar Corcho
SOMEF