Originated from https://bitbucket.org/armish/gsoc14 and will continue here (ToDo).
Unlike many other drug-target databases, this data resource has a controlled vocabulary that can be mapped to BioPAX, for example: 'nutlin 3 results in increased expression of BAX'. Therefore, implementation of a converter first requires a manual mapping from CTD terms to BioPAX ontology. Once the mapping is done, then the actual conversion requires parsing and integrating several CSV files that are distributed by the provider.
- Home page: http://ctdbase.org/
- Type: Drug activity
- Format: XML/CSV
- License: Free for academic use
- Publications: main PMID:27651457, curation PMID:21933848
The converter is structured as a java maven project, where the only major dependencies are Paxtools and JAXB libraries. The project can be compiled into an executable 'fat' JAR file that can be used as a command line utility (described below).
For the conversion, the utility uses three different input files:
- Chemical-Gene Interactions (XML)
- Gene Vocabulary (CSV)
- Chemical Vocabulary (CSV)
all of which can be downloaded from the CTD Downloads page. User can provide any of these files as input and get a BioPAX file as the result of the conversion. If user provides more than one input, then the converted models are merged and a single BioPAX file is provided as output.
The gene/chemical vocabulary converters produce BioPAX file with only
EntityReferences in them. Each entity reference in this converted
models includes the external references provided within the vocabulary file.
From the chemical vocabulary, SmallMoleculeReferences are produced;
and from the gene vocabulary, various types of references are produced
for corresponding CTD gene forms: ProteinReference, DnaReference,
RnaReference, DnaRegionReference and RnaRegionReference.
The interactions file contains all detailed interactions between chemicals and genes, but no background information on the chemical/gene entities.
We can convert any or all of these three files at once, merge into one BioPAX model.
The CTD data sets have nested interactions that are captured by their
structured XML file and their XML schema:
CTD_chem_gene_ixns_structured.xml.gz
and CTD_chem_gene_ixns_structured.xsd.
The converter takes advantage of JAXB library to handle this structured
data set. The automatically generated Java classes that correspond to
this schema can be found under src/main/java/org/ctdbase/model.
The simple flow that show how the conversion happens is available as
the main executable class: CtdToBiopax.java.
Check out (clone) and change the project directory:
$ cd ctd-to-biopax
build with Maven:
$ mvn clean package
This will create an executable JAR file ctd-to-biopax.jar under the
target/ directory. Once you have the single JAR file, you can try
to run without any command line options to see the help text:
$ java -jar ctd-to-biopax.jar
usage: CtdToBiopax
-c,--chemical <arg> CTD chemical vocabulary (CSV) [optional]
-g,--gene <arg> CTD gene vocabulary (CSV) [optional]
-o,--output <arg> Output (BioPAX file) [required]
-r,--remove-dangling Remove dangling utility class entities [optional; use with -x -t]
-t,--taxonomy <arg> filter interactions by species, Taxonomy ID ('9606' for human);
can use special values: 'defined', 'undefined', and 'null') [optional]
-x,--interaction <arg> structured chemical-gene interaction file (XML)
[optional]
Note: the input data files can be compressed, e.g. CTD_genes.csv.gz
If you want to test the converter though, you can download small (old) example files from goal2_ctd_smallSampleInputFiles-20140702.zip. To convert these sample files into a single BioPAX file, run the following command:
$ java -jar ctd-to-biopax.jar -x ctd_small.xml -c CTD_chemicals_small.csv -g CTD_genes_small.csv -r -t 9606 -o ctd.owl
which will create the ctd.owl file for you.