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Overview

This repository hosts the code and data (i.e., ontologies) associated with the paper titled "Bridging the Scientific Knowledge Gap and Reproducibility: A Survey of Provenance, Assertion, and Evidence Ontologies". The paper has been accepted to The Web Conference.

If you find this resource valuable and use it into your work, please consider citing it using the following reference:

@inproceedings{chhetri2025bridging,
  title = {Bridging the Scientific Knowledge Gap and Reproducibility: A Survey of Provenance, Assertion and Evidence Ontologies},
  author = {
    Tek Raj Chhetri and
    Yaroslav O. Halchenko and
    Dorota Jarecka and
    Puja Trivedi and
    Satrajit Ghosh and
    Patrick Ray and
    Lydia Ng
  },
  booktitle = {Companion Proceedings of the ACM Web Conference 2025 (to appear)},
  year = {2025},
  publisher = {ACM},
  address = {Sydney, NSW, Australia}, 
  doi = {10.1145/3701716.3715483},
  isbn = {979-8-4007-1331-6/25/04},
  conference = {ACM Web Conference 2025},
  location = {Sydney, NSW, Australia},
  month = {April 28-May 2}, 
}

Zenodo

The contents of this repository have been permanently archived on Zenodo. We encourage you to cite both our publication and dataset to support reproducibility and further research.

@dataset{chhetri_2025_14879204,
  author       = {Chhetri, Tek Raj and
                  Halchenko, Yaroslav and
                  Jarecka, Dorota and
                  Trivedi, Puja and
                  Ghosh, Satrajit and
                  Ray, Patrick and
                  Ng, Lydia},
  title        = {Dataset: Bridging the Scientific Knowledge Gap and
                   Reproducibility: A Survey of Provenance, Assertion
                   and Evidence Ontologies
                  },
  month        = feb,
  year         = 2025,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.14879204},
  url          = {https://doi.org/10.5281/zenodo.14879204},
}

Contents

  • Data: Contains ontologies related to assertions and evidence. These ontologies provide the necessary modeling to record the assertions and evidence from the various sources, such as scientific publications, experimentation (wet lab).
  • Code: Includes Jupyter Notebook code used for analyzing the ontologies.

List of Ontologies

Acronym Full Name
ECO Evidence and Conclusion Ontology
SIO Semanticscience Integrated Ontology
RDO Reasoning and Discourse Ontology
SEPIO Scientific Evidence and Provenance Information Ontology
AMO Argument Model Ontology
ARGO Arguments Ontology
SWAN Semantic Web Applications in Neuromedicine Ontology
EXPO Ontology of scientific experiments
OBI Ontology for Biomedical Investigations
Nanopublication Nanopublications template ontology
HOH Hierarchies of Hypotheses Ontology
EVI Evidence Graph Ontology
RVO Research Variable Ontology
PAV PAV ontology: provenance, authoring and versioning
OPMW-PROV The Open Provenance Model for Workflows
PROV-O The PROV (provenance) Ontology
P-Plan Ontology for Provenance and Plans
PMLM Provenance for Machine Learning Models (PMLM) ontology
NeuroBridge NeuroBridge ontology
ProPreO Proteomics Data and Process Provenance Ontology (ProPreO)
POEM Psychometric Ontology of Experiences and Measures
PMLM PMLM Ontology
OPMW (or OPMW-PROV) Open Provenance Model for Workflows
HED Hierarchical Event Descriptors Ontology
REPRODUCE-ME REPRODUCE-ME Ontology

List of re-used ontologies

The table below lists ontologies that have been reused by others, such as ECO, which supports the recording of assertions and evidence.

Acronym Full Name Link
CHEBI Chemical Entities of Biological Interest https://www.ebi.ac.uk/chebi/
GO Gene Ontology https://geneontology.org/docs/ontology-documentation/
DC/DC-TERMS Dublin Core Metadata Initiative https://www.dublincore.org/specifications/dublin-core/
NCBITAXON NCBI Organismal Classification https://www.ncbi.nlm.nih.gov/taxonomy
OMRSE Ontology for Modeling and Representation of Social Entities https://www.ebi.ac.uk/ols4/ontologies/omrse
UBERON Uberon Multi-Species Anatomy Ontology https://obofoundry.org/ontology/uberon.html
VO Vaccine Ontology https://www.ebi.ac.uk/ols4/ontologies/vo
IAO Information Artifact Ontology https://obofoundry.org/ontology/iao.html
SO Sequence Ontology http://www.sequenceontology.org/
PR Protein Ontology https://www.ebi.ac.uk/ols4/ontologies/pr
CLO Cell Line Ontology https://bioportal.bioontology.org/ontologies/CLO
OMO OBO Metadata Ontology https://github.com/information-artifact-ontology/ontology-metadata
OGMS Ontology for General Medical Science https://github.com/OGMS/ogms
HP Human Phenotype Ontology https://hpo.jax.org/
IDO Infectious Disease Ontology https://github.com/infectious-disease-ontology/infectious-disease-ontology
OPL Ontology for Parasite Lifecycle https://bioportal.bioontology.org/ontologies/OPL/
OIO Ontology of Biomedical Investigations Ontology of Individuals https://www.ebi.ac.uk/ols4/ontologies/oio
OBA Ontology of Biological Attributes https://github.com/obophenotype/bio-attribute-ontology
PATO Phenotype And Trait OntologyPhenotype And Trait Ontology https://github.com/pato-ontology/pato
CL Cell Ontology https://obofoundry.org/ontology/cl.html
BFO Basic Formal Ontology https://basic-formal-ontology.org/
RO Relation Ontology https://github.com/oborel/obo-relations
COB Core Ontology for Biology and Biomedicine https://bioportal.bioontology.org/ontologies/COB
ENVO Environment Ontology https://sites.google.com/site/environmentontology/
UO Units of Measurement Ontology https://github.com/bio-ontology-research-group/unit-ontology
CHMO Chemical Methods Ontology https://github.com/rsc-ontologies/rsc-cmo
MRO Molecular Role Ontology https://github.com/IEDB/MRO
OBI Ontology for Biomedical Investigations https://www.ebi.ac.uk/ols4/ontologies/obi
STATO Statistical Methods Ontology https://github.com/ISA-tools/stato
PROV-O Provenance Ontology https://www.w3.org/TR/prov-o/
INFO Information Entity Ontology
FOAF Friend of a Friend Ontology http://xmlns.com/foaf/spec/
CiTO Citation Typing Ontology https://sparontologies.github.io/cito/current/cito.html
SKOS Simple Knowledge Organization System https://www.w3.org/2004/02/skos/
VANN Vocabulary Annotation Ontology https://vocab.org/vann/
Taxslim Subset of NCBITAXON -
DAML DARPA Agent Markup Language (DAML+OIL) https://www.daml.org/
vcard vCard Ontology - for describing People and Organizations https://www.w3.org/TR/vcard-rdf/
SWRLA SWRL Annotations http://swrl.stanford.edu/ontologies/3.3/swrla.owl
PROV-O Provenance ontology https://www.w3.org/TR/prov-o/
Schema.org Schema.org https://schema.org/
Bioschemas Bioschemas https://bioschemas.org/
FaBiO FRBR-aligned Bibliographic Ontology https://sparontologies.github.io/fabio/current/fabio.html
DBpedia DBpedia resource http://dbpedia.org/resource
HADatAC HADatAC Vocabulary and Ontology Infrastructure (VSTOI) https://www.hadatac.org/ontologies
SNOMEDCT SNOMED CT clinical terms https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=summary
OPMO Open Provenance Model Vocabulary https://open-biomed.sourceforge.net/opmv/ns.html
OPMV Open Provenance Model Vocabulary https://open-biomed.sourceforge.net/opmv/opmv-guide.html
PROVCARE ProvCaRe ontology https://provcare.case.edu

Mermaid Diagram

The mermaid diagram below illustrates a graphical representation of the ontologies that were reused.

Assertion/Evidence ontolgy

Click here to view the image in a larger size.

Provenance graph

Loading
flowchart TD
    ECO["ECO"] -- reuses --> GO["GO"] & OBI["OBI"] & OIO["OIO"] & CHEBI["CHEBI"] & DC["DC"] & SO["SO"] & NCBITAXON["NCBITAXON"] & PR["PR"] & DublinCore["DublinCore"] & IDO["IDO"] & UBERON["UBERON"] & IAO["IAO"] & PATO["PATO"] & BFO["BFO"] & RO["RO"] & COB["COB"] & UO["UO"] & CHMO["CHMO"] & CL["CL"]
    SIO["SIO"] -- reuses --> DublinCore & FOAF["FOAF"] & CiTO["CiTO"]
    RDO["RDO"] -- reuses --> DublinCore
    SEPIO["SEPIO"] -- reuses --> BFO & COB & GO & IAO & OBI & RO & DublinCore & PATO & STATO["STATO"] & PROV-O["PROV-O"] & FOAF
    AMO["AMO"] -- reuses --> CiTO
    ARGO["ARGO"] -- reuses --> IAO & BFO & INFO["INFO"]
    Nanopublication["Nanopublication"] -- reuses --> DublinCore & SKOS["SKOS"] & VANN["VANN"]
    HOH["HOH"] -- reuses --> DublinCore & CCON["CCON"] & NCIThesaurus["NCIThesaurus"] & BFO & ENVO["ENVO"] & IAO & RO & Taxslim["Taxslim"] & EFO["EFO"]
    EvidenceOntology["EvidenceOntology"] -- reuses --> vCard["vCard"] & DublinCore & DAML["DAML"]
    EVI["EVI"] -- reuses --> PROV-O & Schema.org["Schema.org"] & VANN & SWRLA["SWRLA"] & DublinCore & Bioschemas["Bioschemas"]
    POEM["POEM"] -- reuses --> SIO & STATO & ECO & OBI & VSTOI["VSTOI"] & SNOMEDCT["SNOMEDCT"] & SKOS


Provenance ontolgy

Click here to view the image in a larger size.

Provenance graph

Loading
flowchart TD
    RVO["RVO"] -- reuses --> FaBiO["FaBiO"] & DBPedia["DBPedia"] & DublinCore["DublinCore"] & FOAF["FOAF"]
    PAV["PAV"] -- reuses --> PROV["PROV"] & FOAF & DublinCore
    OPMW["OPMW"] -- reuses --> P-Plan["P-Plan"] & PROV & OPMO["OPMO"] & FOAF & DublinCore & OPMV["OPMV"]
    P-Plan -- reuses --> PROV & VANN["VANN"] & DublinCore
    PMLM["PMLM"] -- reuses --> PROV
    NeuroBridge["NeuroBridge"] -- reuses --> PROV & PROVCARE["PROVCARE"] & SNOMEDCT["SNOMEDCT"]
    HED["HED"] -- reuses --> DublinCore & FOAF
    REPRODUCE-ME["REPRODUCE-ME"] -- reuses --> PROV & P-Plan
    PROPREO["PROPREO"] -- reuses --> DAML["DAML"] & DublinCore


Contact

Acknowledgement

This work is supported by: 1U24MH130918-01 (BICAN knowledge base), NIH-NIBIB P41 EB019936 (ReproNim) and NIH-NIMH R24 MH117295 (DANDI).

License

CC BY 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) License.