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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "BED" in publications use:'
type: software
license: GPL-3.0-only
title: 'BED: Biological Entity Dictionary (BED)'
version: 1.6.0
doi: 10.12688/f1000research.13925.3
identifiers:
- type: doi
  value: 10.32614/CRAN.package.BED
abstract: An interface for the 'Neo4j' database providing mapping between different
  identifiers of biological entities. This Biological Entity Dictionary (BED) has
  been developed to address three main challenges. The first one is related to the
  completeness of identifier mappings. Indeed, direct mapping information provided
  by the different systems are not always complete and can be enriched by mappings
  provided by other resources. More interestingly, direct mappings not identified
  by any of these resources can be indirectly inferred by using mappings to a third
  reference. For example, many human Ensembl gene ID are not directly mapped to any
  Entrez gene ID but such mappings can be inferred using respective mappings to HGNC
  ID. The second challenge is related to the mapping of deprecated identifiers. Indeed,
  entity identifiers can change from one resource release to another. The identifier
  history is provided by some resources, such as Ensembl or the NCBI, but it is generally
  not used by mapping tools. The third challenge is related to the automation of the
  mapping process according to the relationships between the biological entities of
  interest. Indeed, mapping between gene and protein ID scopes should not be done
  the same way than between two scopes regarding gene ID. Also, converting identifiers
  from different organisms should be possible using gene orthologs information. The
  method has been published by Godard and van Eyll (2018) <https://doi.org/10.12688/f1000research.13925.3>.
authors:
- family-names: Godard
  given-names: Patrice
  email: patrice.godard@gmail.com
  orcid: https://orcid.org/0000-0001-6257-9730
preferred-citation:
  type: article
  title: 'BED: a Biological Entity Dictionary based on a graph data model'
  authors:
  - name: Patrice Godard
  - name: Jonathan van Eyll
  journal: F1000Research
  year: '2018'
  volume: '7'
  doi: 10.12688/f1000research.13925.3
  url: https://doi.org/10.12688/f1000research.13925.3
  start: '195'
repository: https://CRAN.R-project.org/package=BED
repository-code: https://github.com/patzaw/BED
url: https://patzaw.github.io/BED/
date-released: '2024-11-09'
contact:
- family-names: Godard
  given-names: Patrice
  email: patrice.godard@gmail.com
  orcid: https://orcid.org/0000-0001-6257-9730