ncRNA-DB
The non-coding RNA human interaction Data Base.

The ncRNA-DB Java package provides
a command-line interface (CLI) and a Java Application Programming Interface (API)
for entity searching and relation retrieval by connecting to the ncRNA-DB on-line data base.

Download

Download the ncRNA-DB Java package. It is both a Java API package and a Java JAR runnable application.
It is released as a Java package to be platform independent and it does not require any external dependency.
See above sections for available CLI commands and for a description of the package structure.

License

The ncRNA-DB CLI and API package is a platform-independent open-source Java package, released under the terms of the LGPL.

CLI (Command-line Interface)

The runnable JAR file provides four commands for querying the on-line ncRNA-DB server instances. They may use to search for biological entity entries in the data base, extract their neighbourhood, extract interactions among or list all the entries of a particular biological type. Entities and relations (interactions) can be referred using the RID (Resource IDentifier) system of ncRNA-DB. Below, a description of the available commands, their behaviours and usage.

Once you have downloaded the JAR file containing the command-line interface, you can run the commands by seeking to the directory where the JAR file is located and typing

java -cp ncrnadb-1.1.jar ncrnadb.cli.COMMAND PARAMETERS

where COMMMAND is one of those listed below, and PARAMETERS are the specific command arguments.

Commands

This is a description fo the available commands in the ncRNA-DB CLI. Please, before read the Documentation, which describe the ncRNA-DB architecture and its resource identifier system (RID). It could be helpful for understanding how RIDs can be used to refers entities and searching for them.

NOTE that all the output formats are tab separated fields, namely fields in the same output row are separated by a tabulation character.

Search biological entities and their synonymous.

java -cp ncrnadb-1.1.jar ncrnadb.cli.Search RID1 RID2 RID3 ...

The Search command searches for the corresponding biological entities in the data base which aliases match the specified RIDs RID1 RID2 RID3 and so on. For each input RID, if a match in the data base have been found, then the application outputs the inputed RID, the list of the entities having such RID (an RID can be used as a non-unique identifing reference, see Documentation) , by their @ORIDs identifiers, and their synonymous RIDs.

java -cp ncrnadb-1.1.jar ncrnadb.cli.Search --file ifile

The Search command searches for the corresponding biological entities in the data base which aliases match the listed RIDs on the file ifile. If the input file contains one RID per row, then the behaviour of the command is the same of that described before. Instead, when multiple RIDs are written in the same line, their matching biological entities are merged in one single output entity. For example, the follow input file

has-let-7a
hsa-let-7a hsa-let-7a-3p

will produce an output like this

-
inputs: ::HSA_LET_7A
synonyms: NCRNA:GENERIC:HSA_LET_7A NCRNA:GENERIC:LET_7A_5P NCRNA:MIRBASE_ACCESSION_NUMBER:MIMAT0000062
EIDs: #14:18588

-
inputs: ::HSA_LET_7A HSA_LET_7A_3P
synonyms: NCRNA:GENERIC:HSA_LET_7A NCRNA:GENERIC:LET_7A_5P NCRNA:MIRBASE_ACCESSION_NUMBER:MIMAT0000062 NCRNA:GENERIC:HSA_LET_7A_3P NCRNA:MIRTARBASE:MIRT038998 NCRNA:MIRTARBASE:MIRT038999 NCRNA:MIRTARBASE:MIRT039000 NCRNA:MIRTARBASE:MIRT039001 NCRNA:MIRTARBASE:MIRT039002 NCRNA:MIRTARBASE:MIRT039003 NCRNA:MIRTARBASE:MIRT039004
EIDs: #14:18588 #14:191440

where EIDs are the internal OrientDB @ORID identifiers of matching biological entities.

Neighborhood of biological entities.

java -cp ncrnadb-1.1.jar ncrnadb.cli.Neighbors RID1 RID2 RID3 ...

java -cp ncrnadb-1.1.jar ncrnadb.cli.Neighbors --file ifile

The command otuputs the interaction-network neighborhood of the specified (by RIDs) entities. See the Search command section, to understand the difference between passing RID1 RID2 RID3 and --file ifile.

For each neighbor, three line are printed in the following format

@V V_ID
#synonyms LIST_OF_SYNONYMS_RIDS
#EIDs LIST_OF_BIOLOGICAL_ENTITY_@ORIDS

where V_ID is a progressive integer number, starting from 0, indentifing the biological entity like a vertex of the output network.

For each existing interaction between two of the matching biological entities, two line are printed in the following format

@E E_ID @ORID
SOURCE INTERACTION_LEVEL PUBMED_ID SUPPORT_SENTENCE

where E_ID is a progressive integer number, starting from 0, indentifing the particular edge relativelly to the output network. @ORID is the internal OrientDB ID, in our server instance, of the edge.

At the end of the file, a series of rows like this, link output entities by their relations (interactions)

@R V_ID1 V_ID2 E_ID

Relations among biological entities.

java -cp ncrnadb-1.1.jar ncrnadb.cli.Relations RID1 RID2 RID3 ...

java -cp ncrnadb-1.1.jar ncrnadb.cli.Relations --file ifile

The Relations command has a similar behaviour of the Neighbors command. Using Neighbors, biological entities which were not specified in the input list of RIDs but that are neighbors of them, are added up to the output set of entities. Instead, using the Relations command, only the relations (interactions) among the input RIDs are printed, and no extra entities are retrieved.

List entity aliases (RIDs) of the ncRNA-DB server instance.

java -cp ncrnadb-1.1.jar ncrnadb.cli.List BIOENTITY_TYPE

where BIOENTITY_TYPE can be one of ncrna, rna, gene, disease, others, all. The command retrieve the complete set of RIDs, belonging to the specified biological entity type.

Java API (Application Programming Interface)

The ncRNA-DB Java implementation is stricly related to the OrientDB Java API and its implementation of the TinkerPop Blueprints standard. The developer can refer to the OrientDB documentation for the version 1.7.9, as well as the OrientDB native Java API which include the Graph API and the Document API.

The package ncrnadb.core provides the ncRNA-DB Java API for connecting to the in-line data base (the ORDB object), and for dealing with the main ncRNA-DB concpets, such as EntityType, RID, Relation, and DataSource. All the Java classes and their methods are documented with Javadoc.

See the ncRNA-DB API Javadoc.

ncRNA-DB - The non-coding RNA human interaction database.