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The DSSTOX mapping file, containing mappings between DTXSIDs and the associated InChI Strings and InChIKeys, greatly facilitated registration into UniChem [135], whereas the DSSTox SDF file made both PubChem (PubChem [136] and ChemSpider registration simple [137].
Finally, a gene-to-protein mapping file and an 'id mapping' file containing different database identifiers for those proteins are provided.
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The generated mapping file contained Tc gene IDs with assigned MapMan bins (gene functional categories).
Such a mapping file contains a < CvReferenceList > element, which contains a list of CVs that are required in an instance data file and a < CvMappingRuleList > element, which contains the mapping rules for the various elements of the data file.
On the tab for generation of true hits (Fig. 1A), the user inputs a tab-delimited plate map file containing reagent identifiers represented by one row per well and a default 'true' value to be assigned to all reagents that are not treated as hits or controls.
Since the map file contains distances between markers on each chromosome, each population's QTLs were mapped to the consensus map separately.
The mapping produced a SAM formatted file containing mapping coordinates, mapping quality, and information on split reads.
KAAS file containing mapping results (.hier) and the transcriptome was annotated against all vertebrate pathways present in the KAAS online server.
The merged sorted.bam file containing mapped reads from the 23 plants and 'genomecov' function in BEDTools (version 2.17.0) [ 39] was used to compute summaries of the aligned sequences coverage for the reference transcriptome.
In addition, the algorithm also requires the input of a file containing a mapping between NCBI taxon IDs and the associated NCBI taxon names.
To populate a pairwise distance matrix of all genes using co-mentioning data, a current file containing a mapping between genes and biomedical literature was downloaded from NCBI FTP site ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2pubmed.gz.gz
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