The Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution.
- Prefix
cdd- Keywords
- annotation classification family and domain databases functional domain image/movie life science literature curation multiple sequence alignment protein protein domain protein structure sequence sequence alignment sequence feature structure
- License
- http://www.nlm.nih.gov/copyright.html
- Links
- Homepage
- Publications
- 2022 The conserved domain database in 2023
- 2016 CDD/SPARCLE: functional classification of proteins via subfamily domain architectures
- 2014 CDD: NCBI's conserved domain database
- 2012 CDD: conserved domains and protein three-dimensional structure
- 2008 CDD: specific functional annotation with the Conserved Domain Database
- https://bioregistry.io/pubmed:17135202
- https://bioregistry.io/pubmed:15215404
- https://bioregistry.io/pubmed:12368255
Identifier Standards
- Pattern for Local Unique Identifiers
-
Local unique identifiers in Conserved Domain Database should match this
regular expression:
^(cd)?\d{5}$ - Example Local Unique Identifier
- cd00400 Resolve
- Pattern for CURIES
-
Compact URIs (CURIEs) constructed from Conserved Domain Database should match
this regular expression:
^cdd:(cd)?\d{5}$ - Example CURIE
- cdd:cd00400
Contacts
- Contact
-
Aron Marchler-Bauer
0000-0003-1516-0712
- Identifier Space Owner
-
National Library of Medicine, Maryland
Ontology
A summary of the relations in the Semantic Farm schema can be found here.
- In Collection (1)
- Synapse.org external links
Mappings to External Registries
Mappings from records in Semantic Farm to external registries comprises the metaregistry. This resource has 10 mappings to external registries with 5 unique external prefixes.
| Registry Name | Registry Metaprefix | External Prefix | Curate |
|---|---|---|---|
| BioContext | biocontext |
CDD
|
|
EDAM
|
edam |
2666
|
|
FAIRSharing
|
fairsharing |
FAIRsharing.b9st5p
|
|
GO
|
go |
CDD
|
|
Integbio
|
integbio |
nbdc00401
|
|
Identifiers.org
|
miriam |
cdd
|
|
N2T
|
n2t |
cdd
|
|
NCBI
|
ncbi |
CDD
|
|
Prefix Commons
|
prefixcommons |
cdd
|
|
UniProt
|
uniprot |
DB-0214
|
Providers
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 cd00400 is used to demonstrate the providers
available for Conserved Domain 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.
| Provider Name | Provider Code | URI |
|---|---|---|
| Conserved Domain Database | cdd |
https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00400 |
| Bioregistry | bioregistry |
https://bioregistry.io/cdd:cd00400 |
| Identifiers.org | miriam |
https://identifiers.org/cdd:cd00400 |
| Name-to-Thing | n2t |
https://n2t.net/cdd:cd00400 |
Extra Providers
Additional providers curated in the Semantic Farm are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.
| Provider Name | Provider Code | URL |
|---|---|---|
| Bio2RDF | bio2rdf |
http://bio2rdf.org/cdd:cd00400 |