In research articles, patents, chemical catalogues, government legislation and textbooks, the use of IUPAC and traditional compound names is universal, despite efforts to introduce more machine-friendly representations such as identifiers and line notations.
In Table 2, the following information is presented: the first column is a line identifier; column W (Warning) represents the types of warnings reported by FindBugs in the mutants; columns ISD, JTI, JTD, JSD, …, represent each one of the 47 μJava operators; column TW(w) is the result of function TW(w) defined in Section 3.1.1.
Table 3 presents the following information: the first column is a line identifier; column W (warnings) represents all bug kinds that have at least one warning related to some mutation point (at line level); columns ISD, JTI, JTD, JSD, …, represent each one of the 47 operators of μJava; columns DCL A (w) and DCL R (w) contain the values of each one of these functions defined in Section 3.1.1.
Line identifiers and gene targets are shown; additional details listed in Table 1.
In that table, the first column is the PubMed identifier (PMID) and each line corresponds to one prediction for that document.
The 'study metadata' section contains study identifier, title, species, cell line, authors, results summary, specification of each study screen, i.e. protocol name and description.
Results are returned as a table with one row per insertion and sortable columns displaying: The internal identifier of the mouse line in the TRACER database.
However, in all cases the auxiliary symbols were contained only in the sequence header, a single line FASTA identifier at the beginning of each file.
Because of the complicated nomenclature that arises in generating identifiers for different lines of mice, for this paper we identify the mice with short-hand abbreviations for vector used (PrP or tet), sequence of Aβ produced (mo or Hu), and co-expressed transgenes (see below) (Additional file 1: Table S1).
For example, all model identifiers can be retrieved (line 4).
All annotation information and significance scores were summarized and concatenated with transcript identifiers into a single line of annotation for each sequence in a Fasta formatted transcriptome file (Additional file 3).
