Registry BioModels Database

BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests.

Prefix: biomodels.db
Alternative Prefixes: BIOMD
Keywords: model
Links: Homepage
Publications: 2006 BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

Identifier Standards

Pattern for Local Unique Identifiers: Local identifiers in BioModels Database should match this regular expression:
^((BIOMD|MODEL)\d{10})|(BMID\d{12})$
Example Local Unique Identifier: BIOMD0000000048 Resolve
Pattern for CURIES: Compact URIs (CURIEs) constructed from BioModels Database should match this regular expression:
^biomodels\.db:((BIOMD|MODEL)\d{10})|(BMID\d{12})$
Example CURIE: biomodels.db:BIOMD0000000048

Contacts

Contact: Michael Hucka 0000-0001-9105-5960 mhucka

Metaregistry BioModels Database

The metaregistry provides mappings between the Bioregistry and other registries. There are 5 mappings to external registries for this resource with 3 unique external prefixes.

Registry Name	Registry Metaprefix	External Prefix
BioContext	`biocontext`	`BIOMODELS.DB`
GO	`go`	`BIOMD`
Identifiers.org	`miriam`	`biomodels.db`
N2T	`n2t`	`biomodels.db`
Prefix Commons	`prefixcommons`	`biomodels`

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 BIOMD0000000048 is used to demonstrate the providers available for BioModels Database. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Name	Metaprefix	URI
BioModels Database	`biomodels.db`	https://www.ebi.ac.uk/biomodels/BIOMD0000000048
Bioregistry	`bioregistry`	https://bioregistry.io/biomodels.db:BIOMD0000000048
Identifiers.org	`miriam`	https://identifiers.org/biomodels.db:BIOMD0000000048
Name-to-Thing	`n2t`	https://n2t.net/biomodels.db:BIOMD0000000048

Extra Providers

Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.

Code	Name	URL
`bio2rdf`	Bio2RDF	http://bio2rdf.org/biomodels:BIOMD0000000048
`omicsdi`	BioModels through OmicsDI	https://www.omicsdi.org/dataset/biomodels/BIOMD0000000048

Normalize prefixes. This can be any capitalization or punctuation variant of the synonyms listed below.

>>> import bioregistry as br
>>> br.normalize_prefix("BIOMD")
'biomodels.db'

Get all synonyms:

>>> import bioregistry as br
>>> br.get_synonyms("biomodels.db")
{'BIOMD'}

This name annotation was originally annotated in Gene Ontology Registry and is redistributed under the CC BY 4.0 license.

Get the name:

>>> import bioregistry as br
>>> br.get_name("biomodels.db")
'BioModels Database'

Get the homepage:

>>> import bioregistry as br
>>> br.get_homepage("biomodels.db")
'https://www.ebi.ac.uk/biomodels/'

Get the contact's name:

>>> import bioregistry as br
>>> br.get_contact_name("biomodels.db")
'Michael Hucka'

Get the contact's email:

>>> import bioregistry as br
>>> br.get_contact_email("biomodels.db")
'mhucka@caltech.edu'

Get the contact's GitHub handle:

>>> import bioregistry as br
>>> br.get_contact_github("biomodels.db")
'mhucka'

Get the contact's ORCiD identifier:

>>> import bioregistry as br
>>> br.get_contact_orcid("biomodels.db")
'0000-0001-9105-5960'