https://github.com/cmungall/obi-mappings

https://github.com/cmungall/obi-mappings

obi obofoundry sssom

Last synced: about 2 months ago
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• Host: GitHub
• URL: https://github.com/cmungall/obi-mappings
• Owner: cmungall
• License: other
• Created: 2021-03-07T21:30:09.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2021-03-07T21:30:18.000Z (almost 4 years ago)
• Last Synced: 2024-10-30T09:25:10.855Z (3 months ago)
• Topics: obi, obofoundry, sssom
• Language: Prolog
• Homepage:
• Size: 17.6 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

        
# OBI mappings

This repo contains experimental AUTOMATED mappings between OBI and other ontologies and ontology-like resources

For context see:

https://github.com/obi-ontology/obi/issues/1304

In future, this may potentially be included in [mapping commons](https://github.com/mapping-commons)

## Inputs

See [downloads](downloads)

 * obi

 * bao

 * mesh

 * wikidata TODO

## Outputs

All mappings are in [SSSOM](https://github.com/mapping-commons/SSSOM), TSV rendering

Currently we use owl:equivalentClass as predicate in the mappings, but this could be skos:exactMatch. The goal is to provide precise 1:1 mappings.

IMPORTANT NOTE: we perform a dedupe step usings sssom-py, but

otherwise we leave in all lexical matches, even low confidence

ones. These are useful for getting a sense of general conceptual

overlap between two resources. In future we will use boomer to reduce

these. For now, pay attention to the confidence score column and

match_category. In general confidence <0.5 is likely to be a false

positive.

See [mappings](mappings)

## Methods

We use rdfmatch

Rules are in conf/

See Makefile

TODO: instructions on how to run with Docker

## MOTIVATION

Mappings are extremely useful for the users of ontologies. It allows users to map annotations from one system to another.

Mappings are also very useful for a gap analysis of ontologies. TODO: add unmapped

## TODO

User boomer to refine mappings