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Scientific Software Registry Collaboration Workshop: From Software Metadata registries to Knowledge Graphs: OntoSoft and OKG-SOFT

dgarijo
dgarijo

In this talk I briefly describe our work in OntoSoft for easy software metadata representation, and how new requirements for software reusability are making us move towards knowledge graphs of scientific software metadata

Scientific Software Registry Collaboration Workshop: From Software Metadata registries to Knowledge Graphs: OntoSoft and OKG-SOFT

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http://mint-project.info
FROM SOFTWARE METADATA
REGISTRIES TO KNOWLEDGE GRAPHS:
ONTOSOFT AND OKG-SOFT
Daniel Garijo, Maximiliano Osorio, Deborah Khider,
Varun Ratnakar and Yolanda Gil
University of Southern California,
Information Sciences Institute
@dgarijov
Scientific Software Registry Collaboration Workshop (SSRCW)
November, 13th 2019
Information
Sciences
Institute
http://mint-project.info
The importance of Scientific Software
2
Open publications
Open data
Open source software
• Software helps understand data
• Provenance, reproducibility
• Software helps understanding methods
• Assumptions, limitations
FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19
Software registries help search, access and understand Scientific Software.
http://mint-project.info
Prior Work: OntoSoft Software Metadata Registry
3
OntoSoft
Distributed Software Metadata Registry
• Complements code repositories to
make them understandable
• Software metadata designed for
scientists
• Metadata is curated by decentralized
communities of users
• Training scientists on best practices
http://ontosoft.org
Finding Software
FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19
[Gil et al 2015]: OntoSoft: Capturing Scientific Software Metadata Eighth ACM International
Conference on Knowledge Capture, Palisades, NY, 2015
http://mint-project.info
Prior Work: OntoSoft Software Metadata Registry
4
FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19
PIHM PIHMgis DrEICH TauDEM WBMsed
Is this enough for Scientific
Software reusability?
http://mint-project.info
Requirements for Software Reusability
5
1. Exposing software inputs, outputs and their corresponding variables
Hydrology Software
Model
FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19
Weather DEM Infiltration
Outflow Error
Input1 Input2 Input3
Output1 Output2
- Land surface temperature (degC)
- Precipitation rate (mm/h)
- Land surface wind speed (m/day)
- Net radiation (MJ/(day m^2))
http://mint-project.info
Requirements for Software Reusability
6
1. Exposing software inputs, outputs and their corresponding variables
2. Capturing the functions of the software component being used
FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19
Hydrology Software Model
Function A: Richards
Equation for water
movement (unsat soil)
Function B: Saint Venant
equations
(shallow water)
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Scientific Software Registry Collaboration Workshop: From Software Metadata registries to Knowledge Graphs: OntoSoft and OKG-SOFT

  • 1. http://mint-project.info FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT Daniel Garijo, Maximiliano Osorio, Deborah Khider, Varun Ratnakar and Yolanda Gil University of Southern California, Information Sciences Institute @dgarijov Scientific Software Registry Collaboration Workshop (SSRCW) November, 13th 2019 Information Sciences Institute
  • 2. http://mint-project.info The importance of Scientific Software 2 Open publications Open data Open source software • Software helps understand data • Provenance, reproducibility • Software helps understanding methods • Assumptions, limitations FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19 Software registries help search, access and understand Scientific Software.
  • 3. http://mint-project.info Prior Work: OntoSoft Software Metadata Registry 3 OntoSoft Distributed Software Metadata Registry • Complements code repositories to make them understandable • Software metadata designed for scientists • Metadata is curated by decentralized communities of users • Training scientists on best practices http://ontosoft.org Finding Software FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19 [Gil et al 2015]: OntoSoft: Capturing Scientific Software Metadata Eighth ACM International Conference on Knowledge Capture, Palisades, NY, 2015
  • 4. http://mint-project.info Prior Work: OntoSoft Software Metadata Registry 4 FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19 PIHM PIHMgis DrEICH TauDEM WBMsed Is this enough for Scientific Software reusability?
  • 5. http://mint-project.info Requirements for Software Reusability 5 1. Exposing software inputs, outputs and their corresponding variables Hydrology Software Model FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19 Weather DEM Infiltration Outflow Error Input1 Input2 Input3 Output1 Output2 - Land surface temperature (degC) - Precipitation rate (mm/h) - Land surface wind speed (m/day) - Net radiation (MJ/(day m^2))
  • 6. http://mint-project.info Requirements for Software Reusability 6 1. Exposing software inputs, outputs and their corresponding variables 2. Capturing the functions of the software component being used FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19 Hydrology Software Model Function A: Richards Equation for water movement (unsat soil) Function B: Saint Venant equations (shallow water)
  • 7. http://mint-project.info Requirements for Software Reusability 7 1. Exposing software inputs, outputs and their corresponding variables 2. Capturing the functions of the software component being used 3. Using principled ontologies with structured names for model variables, processes, and methods FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19 Temp T T_C svo:land_surface_ air__temperature
  • 8. http://mint-project.info Requirements for Software Reusability 8 1. Exposing software inputs, outputs and their corresponding variables 2. Capturing the functions of the software component being used 3. Using principled ontologies with structured names for model variables, processes, and methods 4. Capture the semantic structure of software invocations FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19 Dependencies? Sample runs? Invocation command? Is data supposed to be in the same folder? Default arguments/Configuration files? Volumes? Do I have to log in in the image
  • 9. http://mint-project.info Evolving OntoSoft: Software Description Ontology https://w3id.org/okn/o/sd# Extensions: • Schema.org (software metadata) + Codemeta • W3C Data Cubes (Contents of inputs and outputs) • NASA QUDT (Units) • DockerPedia (Software images) • Scientific Variables Ontology (Standard Variables) FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19 9
  • 10. http://mint-project.info OKG-SOFT: Framework 10 Software Model Catalog contains: • Models from hydrology, agriculture and economy, their versions and model configurations. • More than 200 variables mapped to SVO. • All models are executable through scientific workflows • Most contents are added manually (expert users) collaboratively • Automated unit transformations • Automated software image description • Semi-automated Wikidata linking FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19 https://query.mint.isi.edu/api/mintproject/MINT-ModelCatalogQueries#/ APIs: • SPARQL endpoint • REST APIs (GET/POST) • Python clients
  • 11. http://mint-project.info Exploitation: Exploring Scientific Software Model Metadata 11http://models.mint.isi.edu Explore variables FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19 Explore Software I/O Find Software Models Compare models
  • 12. http://mint-project.info Summary 12 Scientific Software is crucial to understand • Existing data • Published methods Scientific Software Metadata registries help search and understand software • Enough for software reusability? Requirements for scientific software reusability: • Describing inputs, outputs, variables and software invocation details Our approach for capturing and structuring scientific software FROM SOFTWARE METADATA REGISTRIES TO KNOWLEDGE GRAPHS: ONTOSOFT AND OKG-SOFT – SSRCW19