Registry Biofactoid

Biofactoid is a web-based system that empowers authors to capture and share machine-readable summaries of molecular-level interactions described in their publications.

Prefix: biofactoid
Keywords: biocuration biology computational biology crowdsourcing database genetics genomics human biology knowledge representation literature curation molecular biology molecular interaction pathway protein interactions relationships signaling systems biology
License: CC0-1.0
Links: Homepage Repository Request Discussion
Publications: 2021 Author-sourced capture of pathway knowledge in computable form using Biofactoid; 2020 Pathway Commons 2019 Update: integration, analysis and exploration of pathway data; 2021 A flexible search system for high-accuracy identification of biological entities and molecules

Identifier Standards

Pattern for Local Unique Identifiers: Local identifiers in Biofactoid should match this regular expression:
^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
Example Local Unique Identifier: fdb8a927-45c3-48b7-9743-cbb5e16837fa Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from Biofactoid should match this regular expression:
^biofactoid:[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$
Example CURIE: biofactoid:fdb8a927-45c3-48b7-9743-cbb5e16837fa

Contacts

Contact: Jeffrey Wong 0000-0002-8912-5699 jvwong
Contributors: submitter Benjamin M. Gyori 0000-0001-9439-5346 bgyori
Reviewer: Charles Tapley Hoyt 0000-0003-4423-4370 cthoyt

Mappings to External Registries

Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 2 mappings to external registries with 2 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix	Curate
FAIRSharing	`fairsharing`	`FAIRsharing.0ede01`
Identifiers.org	`miriam`	`biofactoid`

Providers

Suggest

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier fdb8a927-45c3-48b7-9743-cbb5e16837fa is used to demonstrate the providers available for Biofactoid. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Provider Name	Provider Code	URI
Biofactoid	`biofactoid`	https://biofactoid.org/document/fdb8a927-45c3-48b7-9743-cbb5e16837fa
Bioregistry	`bioregistry`	https://bioregistry.io/biofactoid:fdb8a927-45c3-48b7-9743-cbb5e16837fa
Identifiers.org	`miriam`	https://identifiers.org/biofactoid:fdb8a927-45c3-48b7-9743-cbb5e16837fa

This name annotation was originally annotated in Bioregistry and is redistributed under the CC0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("biofactoid")
'Biofactoid'

Get the license:

>>> import bioregistry as br
>>> br.get_license("biofactoid")
'CC0-1.0'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("biofactoid")
'https://biofactoid.org'

Get the repository:

>>> import bioregistry as br
>>> br.get_repository("biofactoid")
'https://github.com/PathwayCommons/factoid'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("biofactoid")
'Jeffrey Wong'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("biofactoid")
'jeffvin.wong@utoronto.ca'

Get the contact's GitHub handle:

>>> import bioregistry as br
>>> br.get_contact_github("biofactoid")
'jvwong'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("biofactoid")
'0000-0002-8912-5699'