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},
}
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},
}
- 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.
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 |
The table below lists ontologies that have been reused by others, such as ECO, which supports the recording of assertions and evidence.
The mermaid diagram below illustrates a graphical representation of the ontologies that were reused.
Click here to view the image in a larger size.
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
Click here to view the image in a larger size.
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
- Tek Raj Chhetri [email protected]
This work is supported by: 1U24MH130918-01 (BICAN knowledge base), NIH-NIBIB P41 EB019936 (ReproNim) and NIH-NIMH R24 MH117295 (DANDI).
This work is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) License.