Evidence map›Paper›PMID 39962095›Full record

ArticleScientific data2025

A semantic approach to mapping the Provenance Ontology to Basic Formal Ontology.

Tim Prudhomme, Giacomo De Colle, Austin Liebers, Alec Sculley, Peihong Karl Xie, Sydney Cohen, John Beverley

Abstract read
In one paragraph

Article in Scientific data, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. A fourfold pathogen reference ontology suite.Journal of biomedical semantics · 2025
    Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Tim PrudhommeNational Center for Ontological Research, Buffalo, NY, USA. tmprdh@gmail.com.ORCID http://orcid.org/0000-0003-4143-6524
Giacomo De ColleNational Center for Ontological Research, Buffalo, NY, USA.ORCID http://orcid.org/0000-0002-3600-6506
Austin LiebersNational Center for Ontological Research, Buffalo, NY, USA.ORCID http://orcid.org/0009-0004-1692-3309
Alec SculleyNational Center for Ontological Research, Buffalo, NY, USA.ORCID http://orcid.org/0000-0002-0369-1965
Peihong Karl XieNational Center for Ontological Research, Buffalo, NY, USA.ORCID http://orcid.org/0009-0003-4542-1917
Sydney CohenNational Center for Ontological Research, Buffalo, NY, USA.
John BeverleyNational Center for Ontological Research, Buffalo, NY, USA.ORCID http://orcid.org/0000-0002-1118-1738

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The Provenance Ontology (PROV-O) is a World Wide Web Consortium (W3C) recommended ontology used to structure data about provenance across a wide variety of domains. Basic Formal Ontology (BFO) is a top-level ontology ISO/IEC standard used to structure a wide variety of ontologies, such as the OBO Foundry ontologies and the Common Core Ontologies (CCO). To enhance interoperability between these two ontologies, their extensions, and data organized by them, a mapping methodology and set of alignments are presented according to specific criteria which prioritize semantic and logical principles. The ontology alignments are evaluated by checking their logical consistency with canonical examples of PROV-O instances and querying terms that do not satisfy the alignment criteria as formalized in SPARQL. A variety of semantic web technologies are used in support of FAIR (Findable, Accessible, Interoperable, Reusable) principles.

Identifiers

PMID39962095
PMCPMC11833102

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.