Tools and Features


 

New Features - updated 27 Jan 2015


 

REST API

 

The lncRNAdb REST API has been designed to allow easy programatical access to lncRNAdb content. The API can be catogorised into 3 levels, depending on the amount of requested content and level of detail.

 

LEVEL DESCRIPTION CONTENT EXAMPLE 
1 Returns information 
for a single entry

Single Entry:

  • nomenclature
  • annnotation
  • literature
  • species
  • sequence

Usage 1: http://lncrna.com/rest/<name_of_lncrna> 

Example 1: http://lncrna.com/rest/hotair (Returns all data regarding hotair)

 

Usage 2: http://lncrna.com/rest/hotair/<datatype(s)*> 
(*datatypes are seperated by '/')

Example 2: http://lncrna.com/rest/hotair/annotation/sequence/ 

(Returns only annotation and sequence content for hotair entry)

2 Allows lncRNAdb search.

Multiple Entries:

  • nomenclature
  • annnotation
  • literature
  • species
  • sequence

Usage 1: http://lncrna.com/rest/search/<searchterms>*/
Example 1: http://lncrna.com/rest/search/brain+cancer*/ 
(Returns all data containing words brain and cancer)
Example 2: http://lncrna.com/rest/search/neur/ 
(Returns all data starting with "neur" such as "neuron" and "neural".)

 

Usage 2: 
http://lncrna.com/rest/search/<searchterms>*/<datatype(s)>**
Example 2: 
http://lncrna.com/rest/search/cancer*/nomenclature/literature
(Returns all cancer related information with references)

 

To only obtain specific content of the return results:
*multiple search terms can be joint by '+'
**datatypes are seperated by '/'

3 Retrieves specific information for all entries.

All Entries:

  • nomenclature
  • annnotation
  • literature
  • species
  • sequence

Usage: http://lncrna.com/rest/all/<datatype(s)>

Example: http://lncrna.com/rest/all/literature

(Returns literature references for all entries) 

 

 

 

 

 


 

Sequence Flat File

 

Sequences found in lncrnadb can now be downloaded as a single flat file. 

 

The current version is released on 27 Jan 2015. You can download the file here 

 

he sequence name for each sequences is annotated in the following manner : <lncrnaname>_<species>_<sequence_no> 

 

Hence, using megamind as an example (http://lncrnadb.com/megamind) :

 

 

Sequence Name Corresponding Sequence

megamind_daniorerio_1

sequence 1 of megamind and it refer to sequence from Danio reio

megamind_daniorerio_2

sequence 2 of megamind and it refer to sequence from Danio reio

megamind_homosapiens_3

sequence 3 of megamind and it refer to sequence from Homo sapiens

megamind_homosapiens_4

sequence 4 of megamind and it refer to sequence from Homo sapiens

megamind_musmusculus_5

equence 5 of megamind and it refer to sequence from Mus musculus