analysis of chemicals, diseases, or genes
ctd.pl $input $numerical_column $inType.inputType
#if $inType.inputType == "disease"
$inType.report ANY
#else if $inType.reportType.report == "cgixns"
$inType.reportType.report $inType.reportType.actType
#else
$inType.reportType.report ANY
#end if
$out_file1
**Dataset formats**
The input and output datasets are tabular_.
(`Dataset missing?`_)
.. _tabular: ./static/formatHelp.html#tab
.. _Dataset missing?: ./static/formatHelp.html
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**What it does**
This tool extracts data related to the provided list of identifiers
from the Comparative Toxicogenomics Database (CTD). The fields
extracted vary with the type of data requested; the first row
of the output identifies the columns.
For the curated chemical-gene interactions, you can also choose the
interaction type from the search-and-select box. The choices that
start with '-' are a subset of a choice above them; you can chose
either the general interaction type or a more specific one.
Website: http://ctd.mdibl.org/
-----
**Examples**
- input data file:
HBB
- select Column = c1, Identifier type = Genes, and Data to extract = All disease relationships
- output file::
#Input GeneSymbol GeneName GeneID DiseaseName DiseaseID GeneDiseaseRelation OmimIDs PubMedIDs
hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Ethanol 17676605|18926900
hbb HBB hemoglobin, beta 3043 Abnormalities, Drug-Induced MESH:D000014 inferred via Valproic Acid 8875741
etc.
Another example:
- same input file:
HBB
- select Column = c1, Identifier type = Genes, Data to extract = Curated chemical-gene interactions, and Interaction type = ANY
- output file::
#Input GeneSymbol GeneName GeneID ChemicalName ChemicalID CasRN Organism OrganismID Interaction InteractionTypes PubMedIDs
hbb HBB hemoglobin, beta 3043 1-nitronaphthalene C016614 86-57-7 Macaca mulatta 9544 1-nitronaphthalene metabolite binds to HBB protein binding 16453347
hbb HBB hemoglobin, beta 3043 2,6-diisocyanatotoluene C026942 91-08-7 Cavia porcellus 10141 2,6-diisocyanatotoluene binds to HBB protein binding 8728499
etc.
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**Reference**
Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. (2009)
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for
chemical-gene-disease networks.
Nucleic Acids Res. 37(Database issue):D786-92. Epub 2008 Sep 9.